-
Notifications
You must be signed in to change notification settings - Fork 2
/
bulk-rnaseq.yaml.lock
375 lines (375 loc) · 7.68 KB
/
bulk-rnaseq.yaml.lock
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
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
tools:
- name: sortmerna
owner: rnateam
revisions:
- 10b84b577117
- eb35257d2e29
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: edger
owner: iuc
revisions:
- 070900306913
- 0cb907a2a810
- 334ce9b1bac5
- 3d89af8a44f0
- 555659de7321
- 5bf899c13979
- 6e53e565fc6a
- a8305cf0c951
- ae2aad0a6d50
- d79ed3ec25fe
- df0c8d0a5992
- f2843df56434
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: limma_voom
owner: iuc
revisions:
- 0921444c832d
- 119b069fc845
- 32511f586472
- 58c35179ebf0
- 708348a17fa1
- d6f5fa4ee473
- e827f9aae031
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: qualimap2_bamqc
owner: refinery-platform
revisions:
- a2438e0f1bbf
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: deseq2
owner: iuc
revisions:
- 0696db066a5b
- 6a3a025714d3
- 71bacea10eee
- 7ff33c2d525b
- 8fe98f7094de
- 9a882d108833
- cd9874cb9019
- d027d1f4984e
- de44f8eff84a
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: kallisto_quant
owner: iuc
revisions:
- 10c98fab6c5a
- 2568a3b975cb
- 40985510cd98
- 4f9c4e6566e5
- 60f888039fb2
- c971db6f0fe5
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: salmon
owner: bgruening
revisions:
- 15cd64d7c58b
- 49121db48873
- 6b0ba6de1424
- 7fdb9d1591e2
- b265be7af3db
- c8903f357804
- cc05793bb896
- e3d32471da11
- ebab418107f5
- f4d5237a84f6
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: cutadapt
owner: lparsons
revisions:
- 093678460093
- 104d86c98776
- 135b80fb1ac2
- 288f97432497
- 44e2cc14f75b
- 48f587c13075
- 4e5056fefd88
- 5915ea1ec9b1
- 5eb7e84243f2
- 64172f1c1202
- 660cffd8d92a
- 8c0175e03cee
- 944ae523bacb
- 9845c649f41b
- aa784cb3810d
- b1c926deaa2d
- c053d4cad713
- c4b82dce8335
- c5e2e5902201
- de6cebe3c043
- e4691e1589d3
- fe74900d6dc7
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: multiqc
owner: iuc
revisions:
- 3d93dd18d9f8
- 5e33b465d8d5
- 75c93c70d094
- 9a913cdee30e
- abfd8a6544d7
- b2f1f75d49c4
- bf675f34b056
- c19b16e5729c
- f7985e0479b9
- f7e2f1eb3a16
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: hisat2
owner: iuc
revisions:
- 0c16cad5e03b
- 26371a1df031
- 3fb01a8c902d
- 61ee47027bd3
- 6c19daec423d
- a86e80d3c09c
- d4b55e2beb12
- f4af63aaf57a
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: tophat2
owner: devteam
revisions:
- 16c4255042be
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: sra_tools
owner: iuc
revisions:
- 1ec814014652
- 248f85ff0733
- 4317d3cb6cba
- 494b2ec08162
- 4df8de2d0e48
- 516a54ddf218
- 5e6237d58b0c
- 653e89d73fc4
- 6591f049cf7e
- 69ebb7f46e45
- 6ea73833cf67
- 7068f48d0ef9
- 734abc7ac21d
- 751a694ec620
- 83c7d564b128
- 8848455c0270
- 964579f93c54
- 9a776b080193
- aad3885b3216
- ba931a59dd59
- c441583adae5
- de0f7e0a3896
- e08a7ad4378b
- e407b9da183a
- f5ea3ce9b9b0
- f8054ea1c365
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: rgrnastar
owner: iuc
revisions:
- 3e94726bfa9d
- 3ea5a2a63fa2
- 4014de1b6daf
- 4074fc1940e2
- 44959aa06aeb
- 4df95e2d7f61
- 53255f6eecfc
- 5ec75f5dae3c
- 79de45b5069b
- 7ed2edc1337f
- 850f3679b9b4
- 91e0f03268ca
- 980d2a2e1180
- a2b0feda6933
- b0f2be869d6d
- b9e04854e2bb
- c772497b2c32
- c7c55b694974
- d5659efd66aa
- e132e7d02a3e
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: kallisto_pseudo
owner: iuc
revisions:
- 01247aaf0a10
- 1c75aa5de15e
- 5ae5c312d718
- 87c11c05d238
- a157781cddd7
- ce5d418183c5
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: rmarkdown_wgcna
owner: mingchen0919
revisions:
- 05bcad4b5b4f
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: htseq_count
owner: lparsons
revisions:
- 4418229c501e
- 67b0b160903a
- 7f5a8d427b39
- 916cb26bd9d3
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: fastqc
owner: devteam
revisions:
- 2c64fded1286
- 3d0c7bdf12f5
- 3e1cdf5406db
- 5ec9f6bceaee
- e7b2202befea
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: featurecounts
owner: iuc
revisions:
- 1b851f87fbe0
- 38b6d12edc68
- 6f66ae7c5f7a
- 7db9d3ea71c9
- 90d16db017d7
- a37612abf7f9
- a56fbe2d6ba7
- ce44c6f2ba38
- ea04b737afa0
- f3a5f075498f
- f9d49f5cb597
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: gtf2gene_list
owner: ebi-gxa
revisions:
- 00ee933b08fd
- 040d4b3a19d5
- 14b3f2a4523b
- 1a642de6db01
- 247b439a78f7
- b6354c917ef9
- b95e6a9bb15c
- e255c0e5dfca
tool_panel_section_label: Util
tool_shed_url: toolshed.g2.bx.psu.edu
- name: text_processing
owner: bgruening
revisions:
- 0a8c6b61f0f4
- 12615d397df7
- 86755160afbf
- 9ff72e942410
- d698c222f354
- ddf54b12c295
- f46f0e4f75c4
- fb4ff3c42cd3
- fbf99087e067
tool_panel_section_label: Util
tool_shed_url: toolshed.g2.bx.psu.edu
- name: rseqc
owner: nilesh
revisions:
- 1421603cc95b
- 1a052c827e88
- 27e16a30667a
- 473382134e56
- 5968573462fa
- dbedfc5f5a3c
- f437057e46f1
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: package_qualimap_2_2
owner: refinery-platform
revisions:
- bcc7b19f86fa
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: fastq_quality_filter
owner: devteam
revisions:
- 64e9a6afdd0c
- 7b4468117008
- ce9cd02d5b88
tool_panel_section_label: RNA-Seq
tool_shed_url: toolshed.g2.bx.psu.edu
- name: fastx_artifacts_filter
owner: devteam
revisions:
- 529bccd5e4a1
- d5e9e83cd3d8
tool_panel_section_label: FASTA/FASTQ manipulation
tool_shed_url: toolshed.g2.bx.psu.edu
- name: bowtie2
owner: devteam
revisions:
- 03e9b2fbc005
- 0d4acadabb04
- cd659e8cc5fa
- d5ceb9f3c25b
- f6877ad76b00
tool_panel_section_label: Mapping
tool_shed_url: toolshed.g2.bx.psu.edu
- name: data_manager_refgenie_pull
owner: blankenberglab
revisions:
- 2cb1863cd236
- b2fa406276e7
tool_panel_section_label: Manage Data
tool_shed_url: toolshed.g2.bx.psu.edu
- name: fastq_trimmer_by_quality
owner: devteam
revisions:
- 8050e091e99b
tool_panel_section_label: FASTA/FASTQ manipulation
tool_shed_url: toolshed.g2.bx.psu.edu
- name: fastq_filter_n
owner: ebi-gxa
revisions:
- df87d29fac7f
tool_panel_section_label: FASTA/FASTQ manipulation
tool_shed_url: toolshed.g2.bx.psu.edu
- name: fastq_trim_poly_at
owner: ebi-gxa
revisions:
- ebca4912eabe
tool_panel_section_label: FASTA/FASTQ manipulation
tool_shed_url: toolshed.g2.bx.psu.edu
- name: atlas_fastq_provider
owner: ebi-gxa
revisions:
- 22ce1e7f1aaa
tool_panel_section_label: Get Data
tool_shed_url: toolshed.g2.bx.psu.edu
- name: samtools_view
owner: iuc
revisions:
- 0dbf49c414ae
- 2dce91e11ca7
- 32dc5f781059
- 5826298f6a73
- 6be888be75f9
tool_panel_section_label: SAM/BAM
tool_shed_url: toolshed.g2.bx.psu.edu
- name: fastq_quality_trimmer
owner: ebi-gxa
revisions:
- 27e997d5c273
tool_panel_section_label: FASTA/FASTQ manipulation
tool_shed_url: toolshed.g2.bx.psu.edu
- name: fastq_pair
owner: ebi-gxa
revisions:
- 6e13890afaef
tool_panel_section_label: FASTA/FASTQ manipulation
tool_shed_url: toolshed.g2.bx.psu.edu