-
Notifications
You must be signed in to change notification settings - Fork 25
/
nextflow_schema.json
653 lines (653 loc) · 33.3 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
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/nf-core/mhcquant/master/nextflow_schema.json",
"title": "nf-core/mhcquant pipeline parameters",
"description": "Identify and quantify peptides from mass spectrometry raw data",
"type": "object",
"definitions": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"description": "Input raw / mzML files listed in a tsv file (see help for details)",
"help_text": "Use this to specify a sample sheet table including your input raw or mzml files as well as their meta information such as SampleID and Condition. For example:\n\n| ID | Sample | Condition | ReplicateFileName |\n| -----|:------------:| ----------:|------------------------------------------:|\n| 1 | MM15_Melanom | A | data/MM15_Melanom_W_1_A_standard.raw |\n| 2 | MM15_Melanom | B | data/MM15_Melanom_W_1_B_standard.raw |\n| 3 | MM17_Melanom | B | data/MM17_Melanom_W_1_B_standard.raw |\n\n```bash\n--input 'path/samples.tsv'\n```",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.tsv$",
"fa_icon": "fas fa-file"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"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"
}
}
},
"database_options": {
"title": "Database Options",
"type": "object",
"fa_icon": "fas fa-database",
"description": "Decoy Database generation settings",
"required": ["fasta"],
"properties": {
"fasta": {
"type": "string",
"fa_icon": "fas fa-file",
"pattern": ".fasta$",
"description": "Input FASTA protein database",
"help_text": "Path to the protein database file"
},
"skip_decoy_generation": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Add this parameter when you want to skip the generation of the decoy database.",
"help_text": "If you want to use your own decoys, you can specify a dataset that includes decoy sequences. However, each database entry should keep the prefix 'DECOY_'."
}
}
},
"preprocessing": {
"title": "Spectrum preprocessing",
"type": "object",
"fa_icon": "fas fa-arrows-to-circle",
"description": "Define pre-search settings",
"default": "",
"properties": {
"run_centroidisation": {
"type": "boolean",
"fa_icon": "fas fa-border-center-v",
"default": false,
"description": "Include the flag when the specified ms level is not centroided (default=false). "
},
"pick_ms_levels": {
"type": "integer",
"fa_icon": "fas fa-layer-group",
"default": 2,
"description": "Specify the MS levels for which the peak picking is applied (unless you use `--run_centroidisation`)."
},
"filter_mzml": {
"type": "boolean",
"default": false,
"fa_icon": "fas fa-filter",
"description": "Clean up spectrum files and remove artificial charge 0 peptides."
}
}
},
"search_settings": {
"title": "Database Search Settings",
"type": "object",
"fa_icon": "fas fa-magnifying-glass",
"description": "",
"default": "",
"properties": {
"instrument": {
"type": "string",
"default": "high_res",
"enum": ["high_res", "low_res"],
"hidden": true,
"fa_icon": "fas fa-wrench",
"description": "Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high_res: sum of intensities plus flanking bins, ion trap (low_res) ms/ms: sum of intensities of central M bin only"
},
"enzyme": {
"type": "string",
"fa_icon": "fas fa-scissors",
"default": "unspecific cleavage",
"enum": [
"unspecific cleavage",
"no cleavage",
"Arg-C/P",
"Asp-N",
"Lys-C",
"Lys-N",
"Chymotrypsin",
"CNBr",
"Trypsin",
"Arg-C",
"PepsinA",
"Trypsin/P",
"glutamyl endopeptidase"
],
"description": "Specify which enzymatic restriction should be applied",
"hidden": true,
"help_text": "For HLA peptides rarely other enzymes are used, however most enzymes such as for example 'Trypsin' are available."
},
"activation_method": {
"type": "string",
"fa_icon": "fas fa-star-shooting",
"default": "ALL",
"enum": ["ALL", "CID", "ECD", "ETD", "PQD", "HCD", "IRMPD"],
"description": "Specify which fragmentation method was used in the MS acquisition",
"help_text": "If not specified, `ALL` tries to infer the fragmentation method based on the spectrum file"
},
"digest_mass_range": {
"type": "string",
"fa_icon": "fas fa-line-height",
"description": "Specify the mass range in Dalton that peptides should fulfill to be considered for peptide spectrum matching."
},
"prec_charge": {
"type": "string",
"fa_icon": "fas fa-bolt",
"description": "Specify the precursor charge range that peptides should fulfill to be considered for peptide spectrum matching."
},
"precursor_mass_tolerance": {
"type": "integer",
"fa_icon": "fas fa-think-peaks",
"default": 5,
"description": "Specify the precursor mass tolerance to be used for the Comet database search.",
"help_text": "For high-resolution instruments a precursor mass tolerance value of 5ppm is recommended. (eg. 5)"
},
"precursor_error_units": {
"type": "string",
"fa_icon": "fas fa-think-peaks",
"default": "ppm",
"enum": ["ppm", "Da", "amu"],
"description": "Specify the unit of the precursor mass tolerance to be used for the Comet database search."
},
"fragment_bin_offset": {
"type": "number",
"fa_icon": "fas fa-pipe",
"default": 0.0,
"hidden": true,
"description": "Specify the fragment bin offset to be used for the comet database search.",
"help_text": "For high-resolution instruments a fragment bin offset of 0 is recommended. (See the Comet parameter documentation: https://uwpr.github.io/Comet/parameters/parameters_202401/).\n This parameter needs to be combined with `fragment_bin_tol` parameter"
},
"fragment_mass_tolerance": {
"type": "number",
"default": 0.01,
"fa_icon": "fas fa-pipe",
"description": "Specify the fragment mass tolerance to be used for the comet database search.",
"help_text": "For high-resolution instruments a fragment mass tolerance value of 0.02 is recommended\n(See the Comet parameter documentation: https://uwpr.github.io/Comet/parameters/parameters_202401/).\nThe OpenCometAdapter mulitplies this parameter with 2 to align with other search engines."
},
"number_mods": {
"type": "integer",
"fa_icon": "fas fa-hashtag",
"default": 3,
"description": "Specify the maximum number of modifications that should be contained in a peptide sequence match."
},
"fixed_mods": {
"type": "string",
"fa_icon": "fas fa-cubes-stacked",
"description": "Specify which fixed modifications should be applied to the database search",
"help_text": "e.g. 'Carbamidomethyl (C)' (see OpenMS modifications; for a list of options, see parameter description on https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_CometAdapter.html).\nMultiple modifications can be specified by separating commas:`Oxidation (M),Carbamidomethyl (C)`"
},
"variable_mods": {
"type": "string",
"fa_icon": "fas fa-cubes-stacked",
"default": "Oxidation (M)",
"description": "Specify which variable modifications should be applied to the database search",
"help_text": "e.g. 'Oxidation (M)' (see OpenMS modifications; for a list of options, see parameter description on https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_CometAdapter.html).\nMultiple modifications can be specified by separating commas:`Oxidation (M),Carbamidomethyl (C)`"
},
"num_hits": {
"type": "integer",
"fa_icon": "fas fa-hashtag",
"default": 1,
"description": "Specify the number of hits that should be reported for each spectrum."
},
"use_x_ions": {
"type": "boolean",
"fa_icon": "fas fa-wave-sine",
"description": "Include x ions into the peptide spectrum matching"
},
"use_z_ions": {
"type": "boolean",
"fa_icon": "fas fa-wave-sine",
"description": "Include z ions into the peptide spectrum matching"
},
"use_a_ions": {
"type": "boolean",
"fa_icon": "fas fa-wave-sine",
"description": "Include a ions into the peptide spectrum matching"
},
"use_c_ions": {
"type": "boolean",
"fa_icon": "fas fa-wave-sine",
"description": "Include c ions into the peptide spectrum matching"
},
"use_NL_ions": {
"type": "boolean",
"fa_icon": "fas fa-wave-sine",
"description": "Include NL ions into the peptide spectrum matching"
},
"remove_precursor_peak": {
"type": "boolean",
"fa_icon": "fas fa-pipe",
"description": "Include if you want to remove all peaks around precursor m/z",
"default": false
},
"spectrum_batch_size": {
"type": "integer",
"fa_icon": "fas fa-truck-fast",
"default": 0,
"hidden": true,
"description": "Size of Spectrum batch for Comet processing (Decrease/Increase depending on Memory Availability)"
},
"default_params_file_comet": {
"type": "string",
"fa_icon": "fas fa-file-code",
"hidden": true,
"description": "Specify custom Comet params file. All parameters of this take precedence."
}
}
},
"rescoring_settings": {
"title": "Rescoring settings",
"type": "object",
"fa_icon": "fas fa-star-half-stroke",
"description": "",
"default": "",
"properties": {
"rescoring_engine": {
"type": "string",
"fa_icon": "fas fa-wrench",
"default": "percolator",
"description": "Specify the rescoring engine that should be used for rescoring. Either percolator or mokapot",
"enum": ["percolator", "mokapot"]
},
"feature_generators": {
"type": "string",
"fa_icon": "fas fa-head-side-gear",
"default": "deeplc,ms2pip",
"description": "Specify the feature generator that should be used for rescoring. One or multiple of basic,ms2pip,deeplc,ionmob"
},
"ms2pip_model": {
"type": "string",
"fa_icon": "fas fa-head-side-gear",
"default": "Immuno-HCD",
"enum": [
"Immuno-HCD",
"timsTOF",
"timsTOF2023",
"CID",
"CIDch2",
"CID-TMT",
"TMT",
"HCD",
"HCDch2",
"TTOF5600",
"iTRAQ",
"iTRAQphospho"
],
"description": "Specify the MS²PIP model that should be used for rescoring. Checkout the MS²PIP documentation for available models."
},
"ms2pip_model_dir": {
"type": "string",
"format": "directory-path",
"fa_icon": "fas fa-file-code",
"hidden": true,
"description": "Specify a local directory holding at least the MS²PIP models specified in `ms2pip_model`."
},
"deeplc_calibration_set_size": {
"type": "number",
"fa_icon": "fas fa-head-side-gear",
"hidden": true,
"default": 0.15,
"description": "Specify the number or percentage of PSMs that should be used for calibration of the DeepLC model."
},
"fdr_level": {
"type": "string",
"fa_icon": "fas fa-rectangle-code",
"default": "peptide_level_fdrs",
"description": "Specify the level at which the false discovery rate should be computed.",
"enum": ["peptide_level_fdrs", "psm_level_fdrs", "protein_level_fdrs"]
},
"fdr_threshold": {
"type": "number",
"fa_icon": "fas fa-less-than",
"default": 0.01,
"description": "Specify the false discovery rate threshold at which peptide hits should be selected."
},
"subset_max_train": {
"type": "integer",
"hidden": true,
"default": 0,
"fa_icon": "fas fa-train-track",
"description": "Maximum subset for Percolator training iterations"
}
}
},
"quantification_options": {
"title": "Quantification Options",
"type": "object",
"fa_icon": "fas fa-tally",
"description": "",
"default": "",
"properties": {
"quantify": {
"type": "boolean",
"default": false,
"fa_icon": "fas fa-fast-forward",
"description": "Turn on quantification mode"
},
"max_rt_alignment_shift": {
"type": "integer",
"fa_icon": "fas fa-align-center",
"default": 300,
"description": "Set a maximum retention time shift for the linear RT alignment"
},
"quantification_fdr": {
"type": "boolean",
"hidden": true,
"fa_icon": "fas fa-less-than",
"description": "Compute FDR for the targeted approach",
"help_text": "(Weisser H. and Choudhary J.S. J Proteome Res. 2017 Aug 4)"
},
"quantification_min_prob": {
"type": "number",
"hidden": true,
"default": 0,
"description": "Specify a cut off probability value for quantification events as a filter"
},
"quantification_mz_window": {
"type": "number",
"hidden": true,
"default": 5,
"description": "Specify a m/z window for matching between runs"
},
"quantification_rt_window": {
"type": "number",
"hidden": true,
"default": 0,
"description": "Specify a rt window for matching between runs"
},
"quantification_mapping_tolerance": {
"type": "number",
"hidden": true,
"default": 0,
"description": "Specify a rt mapping tolerance for mapping features between runs"
},
"quantification_peak_width": {
"type": "number",
"hidden": true,
"default": 60,
"description": "Specify a peak width for feature extraction"
},
"quantification_min_peak_width": {
"type": "number",
"hidden": true,
"default": 0.2,
"description": "Specify a minimum peak width for quantification"
}
}
},
"post_processing": {
"title": "Post Processing",
"type": "object",
"fa_icon": "fas fa-waveform-lines",
"description": "",
"default": "",
"properties": {
"peptide_min_length": {
"type": "integer",
"fa_icon": "fas fa-filter",
"default": 8,
"description": "Specify the minimum length of peptides to be considered after processing"
},
"peptide_max_length": {
"type": "integer",
"fa_icon": "fas fa-filter",
"default": 12,
"description": "Specify the maximum length of peptides to be considered after processing"
},
"annotate_ions": {
"type": "boolean",
"default": false,
"fa_icon": "fas fa-tags",
"description": "Create tsv files containing information about the MS2 ion annotations after processing.",
"help_text": "The resulting tsv files should aid in spectrum validation downstream analyses"
}
}
},
"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\\.]+\\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|d|day)\\s*)+$",
"hidden": true,
"help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"help": {
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
},
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"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",
"format": "file-path",
"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"
},
"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
},
"validationShowHiddenParams": {
"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."
},
"validationFailUnrecognisedParams": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters fails when an unrecognised parameter is found.",
"hidden": true,
"help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
},
"validationLenientMode": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters in lenient more.",
"hidden": true,
"help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
},
"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": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/database_options"
},
{
"$ref": "#/definitions/preprocessing"
},
{
"$ref": "#/definitions/search_settings"
},
{
"$ref": "#/definitions/rescoring_settings"
},
{
"$ref": "#/definitions/quantification_options"
},
{
"$ref": "#/definitions/post_processing"
},
{
"$ref": "#/definitions/institutional_config_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/generic_options"
}
]
}