forked from nf-core/rnaseq
-
Notifications
You must be signed in to change notification settings - Fork 0
/
modules.json
313 lines (313 loc) · 15.4 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
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
{
"name": "nf-core/rnaseq",
"homePage": "https://github.com/nf-core/rnaseq",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"bbmap/bbsplit": {
"branch": "master",
"git_sha": "de3e6fc949dcffb8d3508c015f435ace5773ff08",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
"installed_by": ["modules"],
"patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff"
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
"git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"],
"patch": "modules/nf-core/fastp/fastp.diff"
},
"fastqc": {
"branch": "master",
"git_sha": "102cc9b709a6da9f7cee2373563ab1464fca9c0a",
"installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"],
"patch": "modules/nf-core/fastqc/fastqc.diff"
},
"fq/subsample": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules", "fastq_subsample_fq_salmon"]
},
"gffread": {
"branch": "master",
"git_sha": "4ab13872435962dadc239979554d13709e20bf29",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
"installed_by": ["modules"]
},
"hisat2/align": {
"branch": "master",
"git_sha": "a1881f6374506f9e031b7af814768cdb44a6a7d3",
"installed_by": ["fastq_align_hisat2"]
},
"hisat2/build": {
"branch": "master",
"git_sha": "f2f48836bf5c59434966a6c3b2211b29363f31ab",
"installed_by": ["modules"]
},
"hisat2/extractsplicesites": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": ["modules"]
},
"kallisto/index": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"kallisto/quant": {
"branch": "master",
"git_sha": "bdc2a97ced7adc423acfa390742db83cab98c1ad",
"installed_by": ["modules"]
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448",
"installed_by": ["bam_markduplicates_picard"]
},
"preseq/lcextrap": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"qualimap/rnaseq": {
"branch": "master",
"git_sha": "4657d98bc9f565e067c4d924126ce107056f5e2f",
"installed_by": ["modules"],
"patch": "modules/nf-core/qualimap/rnaseq/qualimap-rnaseq.diff"
},
"rsem/calculateexpression": {
"branch": "master",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"]
},
"rsem/preparereference": {
"branch": "master",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"]
},
"rseqc/bamstat": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"],
"patch": "modules/nf-core/rseqc/bamstat/rseqc-bamstat.diff"
},
"rseqc/inferexperiment": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"],
"patch": "modules/nf-core/rseqc/inferexperiment/rseqc-inferexperiment.diff"
},
"rseqc/innerdistance": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"],
"patch": "modules/nf-core/rseqc/innerdistance/rseqc-innerdistance.diff"
},
"rseqc/junctionannotation": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"],
"patch": "modules/nf-core/rseqc/junctionannotation/rseqc-junctionannotation.diff"
},
"rseqc/junctionsaturation": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"],
"patch": "modules/nf-core/rseqc/junctionsaturation/rseqc-junctionsaturation.diff"
},
"rseqc/readdistribution": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"],
"patch": "modules/nf-core/rseqc/readdistribution/rseqc-readdistribution.diff"
},
"rseqc/readduplication": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"],
"patch": "modules/nf-core/rseqc/readduplication/rseqc-readduplication.diff"
},
"rseqc/tin": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["bam_rseqc"],
"patch": "modules/nf-core/rseqc/tin/rseqc-tin.diff"
},
"salmon/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["fastq_subsample_fq_salmon"]
},
"salmon/quant": {
"branch": "master",
"git_sha": "c5b528d0a51c31621b485ab3bcc008f483619ea6",
"installed_by": ["modules", "fastq_subsample_fq_salmon"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
"installed_by": ["bam_stats_samtools"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"bam_markduplicates_picard",
"bam_sort_stats_samtools",
"bam_dedup_stats_samtools_umitools"
]
},
"samtools/sort": {
"branch": "master",
"git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
"installed_by": ["bam_sort_stats_samtools"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": ["bam_stats_samtools"]
},
"sortmerna": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"star/align": {
"branch": "master",
"git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
"installed_by": ["modules"]
},
"star/genomegenerate": {
"branch": "master",
"git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
"installed_by": ["modules"]
},
"stringtie/stringtie": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"subread/featurecounts": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"trimgalore": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
},
"ucsc/bedclip": {
"branch": "master",
"git_sha": "240937a2a9c30298110753292be041188891f2cb",
"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
},
"ucsc/bedgraphtobigwig": {
"branch": "master",
"git_sha": "66290981ab6038ea86177ade40b9449bc790b0ce",
"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
},
"umitools/dedup": {
"branch": "master",
"git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd",
"installed_by": ["bam_dedup_stats_samtools_umitools"],
"patch": "modules/nf-core/umitools/dedup/umitools-dedup.diff"
},
"umitools/extract": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"],
"patch": "modules/nf-core/umitools/extract/umitools-extract.diff"
},
"untar": {
"branch": "master",
"git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
"installed_by": ["modules"]
}
}
},
"subworkflows": {
"nf-core": {
"bam_dedup_stats_samtools_umitools": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
},
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
},
"bam_rseqc": {
"branch": "master",
"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
"installed_by": ["subworkflows"]
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["fastq_align_hisat2"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": [
"bam_sort_stats_samtools",
"bam_markduplicates_picard",
"bam_dedup_stats_samtools_umitools"
]
},
"bedgraph_bedclip_bedgraphtobigwig": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
},
"fastq_align_hisat2": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_fastp": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_trimgalore": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
},
"fastq_subsample_fq_salmon": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
}
}
}
}
}
}