This repository was archived by the owner on Mar 25, 2025. It is now read-only.
forked from AustralianBioCommons/proteinfold
-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathnextflow_schema.json
826 lines (826 loc) · 37.2 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
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
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/nf-core/proteinfold/master/nextflow_schema.json",
"title": "nf-core/proteinfold pipeline parameters",
"description": "Protein 3D structure prediction pipeline",
"type": "object",
"$defs": {
"input_output_options": {
"title": "Global options",
"type": "object",
"fa_icon": "fas fa-coins",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/proteinfold/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"mode": {
"type": "string",
"default": "alphafold2",
"description": "Specifies the mode in which the pipeline will be run. mode can be any combination of ['alphafold2', 'colabfold', 'esmfold'] separated by a comma (',') with no spaces.",
"fa_icon": "fas fa-cogs"
},
"use_gpu": {
"type": "boolean",
"description": "Run on CPUs (default) or GPUs",
"fa_icon": "fas fa-microchip"
},
"split_fasta": {
"type": "boolean",
"description": "Split input multi-fasta file in separated fasta files each of them containing one sequence to be folded",
"fa_icon": "fas fa-microchip"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"multiqc_title": {
"type": "string",
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature"
}
}
},
"alphafold2_options": {
"title": "Alphafold2 options",
"type": "object",
"fa_icon": "fas fa-dna",
"description": "Alphafold2 options.",
"properties": {
"max_template_date": {
"type": "string",
"default": "2020-05-14",
"description": "Maximum date of the PDB templates used by 'AlphaFold2' mode",
"fa_icon": "fas fa-calendar-check"
},
"alphafold2_db": {
"type": "string",
"format": "path",
"exists": true,
"description": "Specifies the DB and PARAMS path used by 'AlphaFold2' mode",
"fa_icon": "fas fa-database"
},
"full_dbs": {
"type": "boolean",
"description": "If true uses the full version of the BFD database otherwise, otherwise it uses its reduced version, small bfd",
"fa_icon": "fas fa-battery-full"
},
"alphafold2_mode": {
"type": "string",
"default": "standard",
"description": "Specifies the mode in which Alphafold2 will be run",
"enum": ["standard", "split_msa_prediction"],
"fa_icon": "fas fa-exchange-alt"
},
"alphafold2_model_preset": {
"type": "string",
"default": "monomer",
"description": "Model preset for 'AlphaFold2' mode",
"enum": ["monomer", "monomer_casp14", "monomer_ptm", "multimer"],
"fa_icon": "fas fa-stream"
}
}
},
"colabfold_options": {
"title": "Colabfold options",
"type": "object",
"fa_icon": "fas fa-coins",
"description": "Colabfold options.",
"properties": {
"colabfold_db": {
"type": "string",
"format": "path",
"exists": true,
"description": "Specifies the PARAMS and DB path used by 'colabfold' mode",
"fa_icon": "fas fa-folder-open"
},
"colabfold_server": {
"type": "string",
"default": "webserver",
"description": "Specifies the MSA server used by Colabfold",
"enum": ["webserver", "local"],
"fa_icon": "fas fa-server"
},
"colabfold_model_preset": {
"type": "string",
"default": "alphafold2_ptm",
"description": "Model preset for 'colabfold' mode",
"enum": [
"auto",
"alphafold2",
"alphafold2_ptm",
"alphafold2_multimer_v1",
"alphafold2_multimer_v2",
"alphafold2_multimer_v3"
],
"fa_icon": "fas fa-stream"
},
"num_recycles_colabfold": {
"type": "integer",
"default": 3,
"description": "Number of recycles for Colabfold",
"fa_icon": "fas fa-recycle"
},
"use_amber": {
"type": "boolean",
"default": true,
"description": "Use Amber minimization to refine the predicted structures",
"fa_icon": "fas fa-compress-alt"
},
"db_load_mode": {
"type": "integer",
"default": 0,
"description": "Specify the way that MMSeqs2 will load the required databases in memory",
"fa_icon": "fas fa-download",
"enum": [0, 1, 2, 3]
},
"host_url": {
"type": "string",
"description": "Specify your custom MMSeqs2 API server url",
"fa_icon": "fas fa-link"
},
"use_templates": {
"type": "boolean",
"default": true,
"description": "Use PDB templates",
"fa_icon": "fas fa-paste"
},
"create_colabfold_index": {
"type": "boolean",
"description": "Create databases indexes when running colabfold_local mode",
"fa_icon": "fas fa-bezier-curve"
}
}
},
"esmfold_options": {
"title": "Esmfold options",
"type": "object",
"fa_icon": "fas fa-coins",
"description": "Esmfold options.",
"properties": {
"esmfold_db": {
"type": "string",
"format": "path",
"exists": true,
"description": "Specifies the PARAMS path used by 'esmfold' mode",
"fa_icon": "fas fa-folder-open"
},
"num_recycles_esmfold": {
"type": "integer",
"default": 4,
"description": "Specifies the number of recycles used by Esmfold",
"fa_icon": "fas fa-server"
},
"esmfold_model_preset": {
"type": "string",
"description": "Specifies whether is a 'monomer' or 'multimer' prediction",
"enum": ["monomer", "multimer"],
"fa_icon": "fas fa-stream",
"default": "monomer"
}
}
},
"foldseek_options": {
"title": "Foldseek options",
"type": "object",
"fa_icon": "fas fa-coins",
"description": "Foldseek options.",
"properties": {
"foldseek_search": {
"type": "string",
"enum": [null, "easysearch"],
"default": null,
"description": "Specifies the mode of foldseek search.",
"fa_icon": "fas fa-search"
},
"foldseek_db": {
"type": "string",
"description": "The ID of Foldseek databases",
"fa_icon": "fas fa-server"
},
"foldseek_db_path": {
"type": "string",
"format": "path",
"exists": true,
"description": "Specifies the path to foldseek databases used by 'foldseek'.",
"fa_icon": "fas fa-folder-open"
},
"foldseek_easysearch_arg": {
"type": "string",
"description": "Specifies the arguments to be passed to foldseek easysearch command",
"fa_icon": "fas fa-server"
}
}
},
"process_skipping_options": {
"title": "Process skipping options",
"type": "object",
"fa_icon": "fas fa-fast-forward",
"description": "Options to skip various steps within the workflow.",
"properties": {
"skip_multiqc": {
"type": "boolean",
"description": "Skip MultiQC.",
"fa_icon": "fas fa-fast-forward"
},
"skip_visualisation": {
"type": "boolean",
"description": "Skip visualisation reports.",
"fa_icon": "fas fa-fast-forward"
}
}
},
"institutional_config_options": {
"title": "Institutional config options",
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
"help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_version": {
"type": "string",
"description": "Git commit id for Institutional configs.",
"default": "master",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"custom_config_base": {
"type": "string",
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
"help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"fa_icon": "fas fa-users-cog"
},
"config_profile_name": {
"type": "string",
"description": "Institutional config name.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_description": {
"type": "string",
"description": "Institutional config description.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_contact": {
"type": "string",
"description": "Institutional config contact information.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_url": {
"type": "string",
"description": "Institutional config URL link.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
}
}
},
"alphafold2_dbs_and_parameters_link_options": {
"title": "Alphafold2 DBs and parameters links options",
"type": "object",
"fa_icon": "fas fa-database",
"description": "Parameters used to provide the links to the DBs and parameters public resources to Alphafold2.",
"properties": {
"bfd_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz",
"description": "Link to BFD dababase",
"fa_icon": "fas fa-link"
},
"small_bfd_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz",
"description": "Link to a reduced version of the BFD dababase",
"fa_icon": "fas fa-link"
},
"alphafold2_params_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar",
"description": "Link to the Alphafold2 parameters",
"fa_icon": "fas fa-link"
},
"mgnify_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/v2.3/mgy_clusters_2022_05.fa.gz",
"description": "Link to the MGnify database",
"fa_icon": "fas fa-link"
},
"pdb70_link": {
"type": "string",
"default": "http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.tar.gz",
"description": "Link to the PDB70 database",
"fa_icon": "fas fa-link"
},
"pdb_mmcif_link": {
"type": "string",
"default": "rsync.rcsb.org::ftp_data/structures/divided/mmCIF/",
"description": "Link to the PDB mmCIF database",
"fa_icon": "fas fa-link"
},
"pdb_obsolete_link": {
"type": "string",
"default": "https://files.wwpdb.org/pub/pdb/data/status/obsolete.dat",
"description": "Link to the PDB obsolete database",
"fa_icon": "fas fa-link"
},
"uniref30_alphafold2_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/v2.3/UniRef30_2021_03.tar.gz",
"description": "Link to the Uniclust30 database",
"fa_icon": "fas fa-link"
},
"uniref90_link": {
"type": "string",
"default": "https://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz",
"description": "Link to the UniRef90 database",
"fa_icon": "fas fa-link"
},
"pdb_seqres_link": {
"type": "string",
"default": "https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt",
"description": "Link to the PDB SEQRES database",
"fa_icon": "fas fa-link"
},
"uniprot_sprot_link": {
"type": "string",
"default": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz",
"description": "Link to the SwissProt UniProt database",
"fa_icon": "fas fa-link"
},
"uniprot_trembl_link": {
"type": "string",
"default": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz",
"description": "Link to the TrEMBL UniProt database",
"fa_icon": "fas fa-link"
}
}
},
"alphafold2_dbs_and_parameters_path_options": {
"title": "Alphafold2 DBs and parameters links options",
"type": "object",
"fa_icon": "fas fa-database",
"description": "Parameters used to provide the paths to the DBs and parameters for Alphafold2.",
"properties": {
"bfd_path": {
"type": "string",
"description": "Path to BFD dababase",
"fa_icon": "fas fa-folder-open",
"default": "null/bfd/*"
},
"small_bfd_path": {
"type": "string",
"description": "Path to a reduced version of the BFD database",
"fa_icon": "fas fa-folder-open",
"default": "null/small_bfd/*"
},
"alphafold2_params_path": {
"type": "string",
"description": "Path to the Alphafold2 parameters",
"fa_icon": "fas fa-folder-open",
"default": "null/alphafold_params_*/*"
},
"mgnify_path": {
"type": "string",
"description": "Path to the MGnify database",
"fa_icon": "fas fa-folder-open",
"default": "null/mgnify/*"
},
"pdb70_path": {
"type": "string",
"description": "Path to the PDB70 database",
"fa_icon": "fas fa-folder-open",
"default": "null/pdb70/**"
},
"pdb_mmcif_path": {
"type": "string",
"description": "Path to the PDB mmCIF database",
"fa_icon": "fas fa-folder-open",
"default": "null/pdb_mmcif/*"
},
"uniref30_alphafold2_path": {
"type": "string",
"description": "Path to the Uniref30 database",
"fa_icon": "fas fa-folder-open",
"default": "null/uniref30/*"
},
"uniref90_path": {
"type": "string",
"description": "Path to the UniRef90 database",
"fa_icon": "fas fa-folder-open",
"default": "null/uniref90/*"
},
"pdb_seqres_path": {
"type": "string",
"description": "Path to the PDB SEQRES database",
"fa_icon": "fas fa-folder-open",
"default": "null/pdb_seqres/*"
},
"uniprot_path": {
"type": "string",
"description": "Path to UniProt database containing the SwissProt and the TrEMBL databases",
"fa_icon": "fas fa-folder-open",
"default": "null/uniprot/*"
}
}
},
"colabfold_dbs_and_parameters_link_options": {
"title": "Colabfold DBs and parameters links options",
"type": "object",
"description": "Parameters used to provide the links to the DBs and parameters public resources to Colabfold.",
"fa_icon": "fas fa-database",
"properties": {
"colabfold_db_link": {
"type": "string",
"default": "http://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz",
"description": "Link to the Colabfold database",
"fa_icon": "fas fa-link"
},
"uniref30_colabfold_link": {
"type": "string",
"default": "https://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2302.tar.gz",
"description": "Link to the UniRef30 database",
"fa_icon": "fas fa-link"
},
"colabfold_alphafold2_params_link": {
"type": "string",
"description": "Link to the Alphafold2 parameters for Colabfold",
"fa_icon": "fas fa-link"
}
}
},
"colabfold_dbs_and_parameters_path_options": {
"title": "Colabfold DBs and parameters links options",
"type": "object",
"description": "Parameters used to provide the links to the DBs and parameters public resources to Colabfold.",
"fa_icon": "fas fa-database",
"properties": {
"colabfold_db_path": {
"type": "string",
"description": "Link to the Colabfold database",
"fa_icon": "fas fa-folder-open",
"default": "null/colabfold_envdb_202108"
},
"uniref30_colabfold_path": {
"type": "string",
"description": "Link to the UniRef30 database",
"fa_icon": "fas fa-folder-open",
"default": "null/uniref30_2302"
},
"colabfold_alphafold2_params_path": {
"type": "string",
"description": "Link to the Alphafold2 parameters for Colabfold",
"fa_icon": "fas fa-folder-open"
},
"colabfold_alphafold2_params_tags": {
"type": "object",
"description": "Dictionary with Alphafold2 parameters tags",
"fa_icon": "fas fa-stream"
}
}
},
"esmfold_parameters_link_options": {
"title": "Esmfold parameters links options",
"type": "object",
"description": "Parameters used to provide the links to the parameters public resources to Esmfold.",
"fa_icon": "fas fa-database",
"properties": {
"esmfold_3B_v1": {
"type": "string",
"default": "https://dl.fbaipublicfiles.com/fair-esm/models/esmfold_3B_v1.pt",
"description": "Link to the Esmfold 3B-v1 model",
"fa_icon": "fas fa-link"
},
"esm2_t36_3B_UR50D": {
"type": "string",
"default": "https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t36_3B_UR50D.pt",
"description": "Link to the Esmfold t36-3B-UR50D model",
"fa_icon": "fas fa-link"
},
"esm2_t36_3B_UR50D_contact_regression": {
"type": "string",
"default": "https://dl.fbaipublicfiles.com/fair-esm/regression/esm2_t36_3B_UR50D-contact-regression.pt",
"description": "Link to the Esmfold t36-3B-UR50D-contact-regression model",
"fa_icon": "fas fa-link"
}
}
},
"esmfold_parameters_path_options": {
"title": "Esmfold parameters links options",
"type": "object",
"description": "Parameters used to provide the links to the parameters public resources to Esmfold.",
"fa_icon": "fas fa-database",
"properties": {
"esmfold_params_path": {
"type": "string",
"description": "Link to the Esmfold parameters",
"fa_icon": "fas fa-folder-open",
"default": "null/*"
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
},
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"hidden": true
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true
},
"max_multiqc_email_size": {
"type": "string",
"description": "File size limit when attaching MultiQC reports to summary emails.",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"default": "25.MB",
"fa_icon": "fas fa-file-upload",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
"help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
},
"multiqc_config": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/plain",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"multiqc_logo": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/plain",
"description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
"fa_icon": "fas fa-image",
"hidden": true
},
"multiqc_methods_description": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/plain",
"description": "Custom MultiQC yaml file containing HTML including a methods description.",
"fa_icon": "fas fa-cog"
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
},
"pipelines_testdata_base_path": {
"type": "string",
"fa_icon": "far fa-check-circle",
"description": "Base URL or local path to location of pipeline test dataset files",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/alphafold2_options"
},
{
"$ref": "#/$defs/colabfold_options"
},
{
"$ref": "#/$defs/esmfold_options"
},
{
"$ref": "#/$defs/foldseek_options"
},
{
"$ref": "#/$defs/process_skipping_options"
},
{
"$ref": "#/$defs/institutional_config_options"
},
{
"$ref": "#/$defs/alphafold2_dbs_and_parameters_link_options"
},
{
"$ref": "#/$defs/alphafold2_dbs_and_parameters_path_options"
},
{
"$ref": "#/$defs/colabfold_dbs_and_parameters_link_options"
},
{
"$ref": "#/$defs/colabfold_dbs_and_parameters_path_options"
},
{
"$ref": "#/$defs/esmfold_parameters_link_options"
},
{
"$ref": "#/$defs/esmfold_parameters_path_options"
},
{
"$ref": "#/$defs/generic_options"
}
],
"properties": {
"helixfold3_init_models_link": {
"type": "string",
"default": "https://paddlehelix.bd.bcebos.com/HelixFold3/params/HelixFold3-params-240814.zip"
},
"helixfold3_init_models_path": {
"type": "string",
"default": "null/HelixFold3-240814.pdparams"
},
"helixfold3_db": {
"type": "string"
},
"helixfold3_uniclust30_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/casp14_versions/uniclust30_2018_08_hhsuite.tar.gz"
},
"helixfold3_ccd_preprocessed_link": {
"type": "string",
"default": "https://paddlehelix.bd.bcebos.com/HelixFold3/CCD/ccd_preprocessed_etkdg.pkl.gz"
},
"helixfold3_rfam_link": {
"type": "string",
"default": "https://paddlehelix.bd.bcebos.com/HelixFold3/MSA/Rfam-14.9_rep_seq.fasta"
},
"helixfold3_bfd_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz"
},
"helixfold3_small_bfd_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz"
},
"helixfold3_pdb_seqres_link": {
"type": "string",
"default": "https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt"
},
"helixfold3_uniref90_link": {
"type": "string",
"default": "ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz"
},
"helixfold3_mgnify_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/casp14_versions/mgy_clusters_2018_12.fa.gz"
},
"helixfold3_pdb_mmcif_link": {
"type": "string",
"default": "rsync.rcsb.org::ftp_data/structures/divided/mmCIF/"
},
"helixfold3_uniclust30_path": {
"type": "string",
"default": "null/uniclust30/*"
},
"helixfold3_ccd_preprocessed_path": {
"type": "string",
"default": "null/ccd_preprocessed_etkdg.pkl.gz"
},
"helixfold3_rfam_path": {
"type": "string",
"default": "null/Rfam-14.9_rep_seq.fasta"
},
"helixfold3_bfd_path": {
"type": "string",
"default": "null/bfd/*"
},
"helixfold3_small_bfd_path": {
"type": "string",
"default": "null/small_bfd/*"
},
"helixfold3_uniprot_path": {
"type": "string",
"default": "null/uniprot/*"
},
"helixfold3_pdb_seqres_path": {
"type": "string",
"default": "null/pdb_seqres/*"
},
"helixfold3_uniref90_path": {
"type": "string",
"default": "null/uniref90/*"
},
"helixfold3_mgnify_path": {
"type": "string",
"default": "null/mgnify/*"
},
"helixfold3_pdb_mmcif_path": {
"type": "string",
"default": "null/pdb_mmcif/*"
},
"helixfold3_uniprot_sprot_link": {
"type": "string",
"default": "ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"
},
"helixfold3_uniprot_trembl_link": {
"type": "string",
"default": "ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz"
},
"helixfold3_pdb_obsolete_link": {
"type": "string",
"default": "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat"
},
"helixfold3_maxit_src_path": {
"type": "string",
"default": "null/maxit-v11.200-prod-src"
},
"rosettafold_all_atom_db": {
"type": "string"
},
"uniref30_rosettafold_all_atom_link": {
"type": "string",
"default": "http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz"
},
"pdb100_rosettafold_all_atom_link": {
"type": "string",
"default": "https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz"
},
"bfd_rosettafold_all_atom_path": {
"type": "string",
"default": "null/bfd/*"
},
"rfaa_paper_weights_link": {
"type": "string",
"default": "http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFAA_paper_weights.pt"
},
"uniref30_rosettafold_all_atom_path": {
"type": "string",
"default": "null/uniref30/UniRef30_2020_06/*"
},
"pdb100_rosettafold_all_atom_path": {
"type": "string",
"default": "null/pdb100_2021Mar03/*"
},
"rfaa_paper_weights_path": {
"type": "string",
"default": "null/RFAA_paper_weights.pt"
},
"bfd_rosettafold_all_atom_link": {
"type": "string",
"default": "https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz"
}
}
}