forked from nf-core/proteinfold
-
Notifications
You must be signed in to change notification settings - Fork 0
/
nextflow_schema.json
568 lines (568 loc) · 27.9 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
{
"$schema": "http://json-schema.org/draft-07/schema",
"$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",
"definitions": {
"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",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"schema": "assets/schema_input.json",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/proteinfold/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"mode": {
"type": "string",
"default": "alphafold2",
"description": "Specifies the mode in which the pipeline will be run",
"enum": ["alphafold2", "colabfold"],
"fa_icon": "fas fa-cogs"
},
"use_gpu": {
"type": "boolean",
"description": "Run on CPUs (default) or GPUs",
"fa_icon": "fas fa-microchip"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"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",
"description": "Specifies the DB and PARAMS path used by 'AlphaFold2' mode",
"fa_icon": "fas fa-database"
},
"full_dbs": {
"type": "boolean",
"default": false,
"description": "If true uses full DBs otherwise, otherwise it uses the reduced version of DBs",
"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_ptm",
"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",
"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": ["AlphaFold2-ptm", "AlphaFold2-multimer-v1", "AlphaFold2-multimer-v2"],
"fa_icon": "fas fa-stream"
},
"num_recycle": {
"type": "integer",
"default": 3,
"description": "Number of recycles",
"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"
}
}
},
"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"
}
}
},
"max_job_request_options": {
"title": "Max job request options",
"type": "object",
"fa_icon": "fab fa-acquisitions-incorporated",
"description": "Set the top limit for requested resources for any single job.",
"help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
"properties": {
"max_cpus": {
"type": "integer",
"description": "Maximum number of CPUs that can be requested for any single job.",
"default": 16,
"fa_icon": "fas fa-microchip",
"hidden": true,
"help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
},
"max_memory": {
"type": "string",
"description": "Maximum amount of memory that can be requested for any single job.",
"default": "128.GB",
"fa_icon": "fas fa-memory",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"hidden": true,
"help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
},
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job.",
"default": "240.h",
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
"hidden": true,
"help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
}
}
},
"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": {
"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": {
"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": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold/alphafold_params_2022-03-02.tar",
"description": "Link to the Alphafold2 parameters",
"fa_icon": "fas fa-link"
},
"mgnify": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/casp14_versions/mgy_clusters_2018_12.fa.gz",
"description": "Link to the MGnify database",
"fa_icon": "fas fa-link"
},
"pdb70": {
"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": {
"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": {
"type": "string",
"default": "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat",
"description": "Link to the PDV obsolete database",
"fa_icon": "fas fa-link"
},
"uniclust30": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/casp14_versions/uniclust30_2018_08_hhsuite.tar.gz",
"description": "Link to the Uniclust30 database",
"fa_icon": "fas fa-link"
},
"uniref90": {
"type": "string",
"default": "ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz",
"description": "Link to the UniRef90 database",
"fa_icon": "fas fa-link"
},
"pdb_seqres": {
"type": "string",
"default": "ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt",
"description": "Link to the PDB SEQRES database",
"fa_icon": "fas fa-link"
},
"uniprot_sprot": {
"type": "string",
"default": "ftp://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": {
"type": "string",
"default": "ftp://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"
},
"small_bfd_path": {
"type": "string",
"description": "Path to a reduced version of the BFD database",
"fa_icon": "fas fa-folder-open"
},
"alphafold2_params_path": {
"type": "string",
"description": "Path to the Alphafold2 parameters",
"fa_icon": "fas fa-folder-open"
},
"mgnify_path": {
"type": "string",
"description": "Path to the MGnify database",
"fa_icon": "fas fa-folder-open"
},
"pdb70_path": {
"type": "string",
"description": "Path to the PDB70 database",
"fa_icon": "fas fa-folder-open"
},
"pdb_mmcif_path": {
"type": "string",
"description": "Path to the PDB mmCIF database",
"fa_icon": "fas fa-folder-open"
},
"uniclust30_path": {
"type": "string",
"description": "Path to the Uniclust30 database",
"fa_icon": "fas fa-folder-open"
},
"uniref90_path": {
"type": "string",
"description": "Path to the UniRef90 database",
"fa_icon": "fas fa-folder-open"
},
"pdb_seqres_path": {
"type": "string",
"description": "Path to the PDB SEQRES database",
"fa_icon": "fas fa-folder-open"
},
"uniprot_path": {
"type": "string",
"description": "Path to UniProt database containing the SwissProt and the TrEMBL databases",
"fa_icon": "fas fa-folder-open"
}
}
},
"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": {
"type": "string",
"default": "http://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2103.tar.gz",
"description": "Link to the UniRef30 database",
"fa_icon": "fas fa-link"
},
"colabfold_alphafold2_params": {
"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"
},
"uniref30_path": {
"type": "string",
"description": "Link to the UniRef30 database",
"fa_icon": "fas fa-folder-open"
},
"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"
}
}
},
"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": {
"help": {
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"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",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"multiqc_logo": {
"type": "string",
"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",
"description": "Custom MultiQC yaml file containing HTML including a methods description.",
"fa_icon": "fas fa-cog"
},
"tracedir": {
"type": "string",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"default": "${params.outdir}/pipeline_info",
"fa_icon": "fas fa-cogs",
"hidden": true
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
},
"show_hidden_params": {
"type": "boolean",
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/alphafold2_options"
},
{
"$ref": "#/definitions/colabfold_options"
},
{
"$ref": "#/definitions/institutional_config_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/alphafold2_dbs_and_parameters_link_options"
},
{
"$ref": "#/definitions/alphafold2_dbs_and_parameters_path_options"
},
{
"$ref": "#/definitions/colabfold_dbs_and_parameters_link_options"
},
{
"$ref": "#/definitions/colabfold_dbs_and_parameters_path_options"
},
{
"$ref": "#/definitions/generic_options"
}
]
}