-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathnextflow_schema.json
724 lines (724 loc) · 32.9 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
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
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/vmikk/PhyloNext/main/nextflow_schema.json",
"title": "PhyloNext pipeline parameters",
"description": "A pipeline for phylogenetic diversity analysis of GBIF-mediated 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"],
"properties": {
"input": {
"type": "string",
"format": "directory-path",
"mimetype": "text/csv",
"schema": "assets/schema_input.json",
"description": "Path to the directory with parquet files (GBIF occurrence dump)",
"help_text": "Input data should be in the Parquet format. Could be stored locally or in the cloud (S3 or Azure Blob storage).",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"description": "The output directory where the results will be saved",
"default": "./results",
"fa_icon": "fas fa-folder-open"
},
"phytree": {
"type": "string",
"fa_icon": "fas fa-tree",
"description": "Custom phylogenetic tree in the Newick of Nexus format",
"format": "file-path",
"mimetype": "text/x-nh",
"pattern": ".nwk$|.{n,N}ewick$|.tre$|.tree$|.nex$|.{n,N}exus$|.nxs$",
"help_text": "Tips should be labeled either with Latin binomials (e.g., \"Homo_sapiens\"), or with Open Tree IDs (e.g, \"ott359899\"). Please adjust the `--phylabels` parameter correspondingly."
}
}
},
"taxonomic_scope": {
"title": "Taxonomic scope",
"type": "object",
"description": "Define which taxa should be analyzed",
"default": "",
"fa_icon": "fas fa-cat",
"properties": {
"phylum": {
"type": "string",
"fa_icon": "fas fa-cat",
"description": "Phylum to analyze (multiple comma-separated values allowed); e.g., \"Chordata\""
},
"classis": {
"type": "string",
"fa_icon": "fas fa-cat",
"description": "Class to analyze (multiple comma-separated values allowed); e.g., \"Mammalia\""
},
"order": {
"type": "string",
"fa_icon": "fas fa-cat",
"description": "Order to analyze (multiple comma-separated values allowed); e.g., \"Carnivora\""
},
"family": {
"type": "string",
"fa_icon": "fas fa-cat",
"description": "Family to analyze (multiple comma-separated values allowed); e.g., \"Felidae,Canidae\""
},
"genus": {
"type": "string",
"fa_icon": "fas fa-cat",
"description": "Genus to analyze (multiple comma-separated values allowed); e.g., \"Felis,Canis,Lynx\""
},
"specieskeys": {
"type": "string",
"fa_icon": "fas fa-tasks",
"description": "Custom list of GBIF specieskeys (file with a single column)",
"format": "file-path",
"mimetype": "text/plain",
"pattern": ".txt^"
},
"noextinct": {
"type": "string",
"fa_icon": "fas fa-bacteria",
"format": "file-path",
"mimetype": "text/plain",
"description": "File with extinct species specieskeys for their removal (file with a single column, with header)",
"pattern": ".txt^"
},
"excludehuman": {
"type": "boolean",
"fa_icon": "fas fa-user-alt-slash",
"description": "Logical, exclude genus \"Homo\" from occurrence data (default, true)",
"default": true
}
}
},
"spatial_scope": {
"title": "Spatial scope",
"type": "object",
"description": "Spatial filters",
"default": "",
"fa_icon": "fas fa-globe",
"properties": {
"latmin": {
"type": "number",
"fa_icon": "fas fa-globe",
"description": "Minimum latitude of species occurrences (decimal degrees); e.g., 5.1"
},
"latmax": {
"type": "number",
"fa_icon": "fas fa-globe",
"description": "Maximum latitude of species occurrences (decimal degrees); e.g., 15.5"
},
"lonmin": {
"type": "number",
"fa_icon": "fas fa-globe",
"description": "Minimum longitude of species occurrences (decimal degrees); e.g., 47.0"
},
"lonmax": {
"type": "number",
"fa_icon": "fas fa-globe",
"description": "Maximum longitude of species occurrences (decimal degrees); e.g., 55.5"
},
"country": {
"type": "string",
"fa_icon": "fas fa-flag",
"description": "Country code, ISO 3166 (multiple comma-separated values allowed); e.g., \"DE,PL,CZ\""
},
"polygon": {
"type": "string",
"default": "None",
"fa_icon": "fas fa-draw-polygon"
},
"wgsrpd": {
"type": "string",
"fa_icon": "fas fa-globe-americas",
"default": "null",
"format": "file-path",
"description": "Polygons of World Geographical Regions; e.g., \"pipeline_data/WGSRPD.RData\""
},
"regions": {
"type": "string",
"fa_icon": "fas fa-globe-americas",
"description": "Names of World Geographical Regions; e.g., \"L1_EUROPE,L1_ASIA_TEMPERATE\""
}
}
},
"spatial_outliers_removal": {
"title": "Spatial outliers removal",
"type": "object",
"description": "",
"default": "",
"properties": {
"dbscan": {
"type": "boolean",
"fa_icon": "fas fa-cookie",
"description": "Logical, remove spatial outliers with density-based clustering; e.g., \"false\""
},
"dbscannoccurrences": {
"type": "integer",
"fa_icon": "fas fa-cookie",
"description": "Minimum species occurrence to perform DBSCAN; e.g., 30",
"default": 30
},
"dbscanepsilon": {
"type": "integer",
"fa_icon": "fas fa-cookie",
"description": "DBSCAN parameter epsilon, km; e.g., \"700\"",
"default": 1500
},
"dbscanminpts": {
"type": "integer",
"fa_icon": "fas fa-cookie",
"description": "DBSCAN min number of points; e.g., \"3\"",
"default": 3
}
},
"fa_icon": "fas fa-cookie"
},
"occurrence_filtering_and_binning": {
"title": "Occurrence filtering and binning",
"type": "object",
"description": "",
"default": "",
"fa_icon": "fas fa-filter",
"properties": {
"minyear": {
"type": "integer",
"fa_icon": "fas fa-clock",
"description": "Minimum year of record's occurrences; e.g., 1945",
"default": 1945
},
"maxyear": {
"type": "string",
"default": null,
"fa_icon": "fas fa-clock"
},
"basisofrecordinclude": {
"type": "string",
"default": "None",
"help_text": "For details, see description of a Darwin Core term [Basis of record](https://docs.gbif.org/course-data-use/en/basis-of-record.html).",
"fa_icon": "fas fa-clipboard",
"description": "Basis of record to include from the data (default, all); e.g., \"PRESERVED_SPECIMEN\""
},
"basisofrecordexclude": {
"type": "string",
"default": "FOSSIL_SPECIMEN,LIVING_SPECIMEN",
"help_text": "For details, see description of a Darwin Core term [Basis of record](https://docs.gbif.org/course-data-use/en/basis-of-record.html).",
"description": "Basis of record to exclude from the data; e.g., \"FOSSIL_SPECIMEN,LIVING_SPECIMEN\" (default)",
"fa_icon": "fas fa-clipboard"
},
"coordprecision": {
"type": "number",
"default": 0.1,
"fa_icon": "fas fa-map-marked",
"description": "Coordinate precision threshold (less than)"
},
"coorduncertainty": {
"type": "integer",
"default": 10000,
"fa_icon": "fas fa-map-marked",
"description": "Maximum allowed coordinate uncertainty, meters"
},
"coorduncertaintyexclude": {
"type": "string",
"default": "301,3036,999,9999",
"fa_icon": "fas fa-map-marked",
"description": "Black list of coordinate uncertainty values"
},
"h3resolution": {
"type": "integer",
"default": 4,
"fa_icon": "fas fa-cubes",
"description": "Spatial resolution of the H3 geospatial indexing system; e.g., 4",
"minimum": 1,
"maximum": 9
},
"roundcoords": {
"type": "integer",
"fa_icon": "fas fa-search",
"description": "Numeric, round spatial coordinates to N decimal places, to reduce the dataset size (default, 2; set to negative to disable rounding)",
"default": 2
}
}
},
"coordinatecleaner_like_filtering": {
"title": "CoordinateCleaner-like filtering",
"type": "object",
"description": "Removal of common spatial errors",
"default": "",
"fa_icon": "fas fa-object-group",
"properties": {
"terrestrial": {
"type": "string",
"default": "params.data_path + \"/Land_Buffered_025_dgr.RData\"",
"fa_icon": "fas fa-road",
"description": "Land polygon for removal of non-terrestrial occurrences; e.g., \"pipeline_data/Land_Buffered_025_dgr.RData\"",
"format": "file-path"
},
"rmcountrycentroids": {
"type": "string",
"fa_icon": "far fa-building",
"description": "Polygons with country and province centroids; e.g., \"pipeline_data/CC_CountryCentroids_buf_1000m.RData\"",
"format": "file-path",
"default": "null"
},
"rmcountrycapitals": {
"type": "string",
"fa_icon": "fas fa-city",
"description": "Polygons with country capitals; e.g., \"pipeline_data/CC_Capitals_buf_10000m.RData\"",
"format": "file-path",
"default": "null"
},
"rminstitutions": {
"type": "string",
"fa_icon": "fas fa-laptop-house",
"description": "Polygons with biological institutions and museums; e.g., \"pipeline_data/CC_Institutions_buf_100m.RData\"",
"format": "file-path",
"default": "null"
},
"rmurban": {
"type": "string",
"fa_icon": "fas fa-city",
"description": "Polygons with urban areas; e.g., \"pipeline_data/CC_Urban.RData\"",
"format": "file-path",
"default": "null"
}
}
},
"biodeverse": {
"title": "Biodeverse",
"type": "object",
"description": "Diversity indices",
"default": "",
"properties": {
"indices": {
"type": "string",
"default": "calc_richness,calc_simpson_shannon,calc_endemism_whole,calc_pd,calc_pe,calc_phylo_rpd1,calc_phylo_rpd2,calc_phylo_rpe1,calc_phylo_rpe2",
"description": "Comma-seprated list of diversity and endemism indices; e.g., \"calc_richness,calc_pd,calc_pe\"",
"fa_icon": "fas fa-cogs"
},
"iterations": {
"type": "integer",
"default": 1000,
"description": "Number of randomisation iterations; e.g., 1000",
"fa_icon": "fas fa-cogs"
},
"biodiversethreads": {
"type": "integer",
"default": 10,
"description": "Number of Biodiverse threads; e.g., 10",
"fa_icon": "fas fa-cogs"
},
"randname": {
"type": "string",
"default": "rand_structured",
"fa_icon": "fas fa-cogs",
"description": "Randomisation scheme type; e.g., \"rand_structured\"",
"enum": ["rand_structured"]
},
"randconstrain": {
"type": "string",
"default": "None",
"fa_icon": "fas fa-cogs"
}
},
"fa_icon": "fas fa-cogs"
},
"visualization_interactive": {
"title": "Visualization - interactive",
"type": "object",
"description": "Leaflet-based map parameters",
"default": "",
"properties": {
"leaflet_var": {
"type": "string",
"default": "RICHNESS_ALL,PD,SES_PD,PD_P,ENDW_WE,SES_ENDW_WE,PE_WE,SES_PE_WE,CANAPE,Redundancy",
"fa_icon": "fas fa-atlas",
"description": "Variables to plot; e.g., \"RICHNESS_ALL,PD,SES_PD,PD_P,ENDW_WE,SES_ENDW_WE,PE_WE,SES_PE_WE,CANAPE,Redundancy\""
},
"leaflet_canapesuper": {
"type": "boolean",
"fa_icon": "fas fa-atlas",
"description": "Include the `superendemism` class in CANAPE results"
},
"leaflet_color": {
"type": "string",
"default": "RdYlBu",
"fa_icon": "fas fa-atlas",
"description": "Color scheme for continuous variables (default, \"RdYlBu\")",
"enum": [
"RdYlBu",
"Blues",
"BrBG",
"BuGn",
"BuPu",
"GnBu",
"Greens",
"Greys",
"Oranges",
"OrRd",
"PiYG",
"PRGn",
"PuBu",
"PuBuGn",
"PuOr",
"PuRd",
"Purples",
"RdBu",
"RdGy",
"RdPu",
"RdYlGn",
"Reds",
"Spectral",
"YlGn",
"YlGnBu",
"YlOrBr",
"YlOrRd",
"Accent",
"viridis",
"inferno",
"plasma",
"magma"
],
"help_text": "The name of a preset palette from the `RColorBrewer` package."
},
"leaflet_palette": {
"type": "string",
"default": "quantile",
"fa_icon": "fas fa-atlas",
"description": "Color palette for continuous variables (default, \"quantile\")",
"enum": ["quantile", "equal", "continuous"],
"help_text": "Defines mapping of data values to colors . See [Leaflet docs](https://rstudio.github.io/leaflet/colors.html):<br>\n`colorNumeric` is a simple linear mapping from continuous numeric data to an interpolated palette.<br>\n`colorBin` also maps continuous numeric data, but performs binning based on value (see the cut function). <br>\n`colorQuantile` similarly bins numeric data, but via the quantile function."
},
"leaflet_bins": {
"type": "integer",
"default": 5,
"fa_icon": "fas fa-atlas",
"description": "Number of color bins for continuous variables (default, 5)"
},
"leaflet_redundancy": {
"type": "number",
"default": 0,
"fa_icon": "fas fa-atlas",
"description": "Redundancy threshold for hiding the grid cells with low number of records (default, 0 = display all grid cells)",
"minimum": 0,
"maximum": 1,
"help_text": "Sampling redundancy = [1 \u2013 (richness / number of specimens)] in a grid cell."
},
"leaflet_sescolor": {
"type": "string",
"default": "threat",
"fa_icon": "fas fa-atlas",
"description": "Color scheme for standardized effect sizes, SES",
"help_text": "default, \"threat\"; alternative - \"hotspots"
}
},
"fa_icon": "fas fa-passport"
},
"visualization_static": {
"title": "Visualization - static",
"type": "object",
"description": "Static maps",
"default": "",
"fa_icon": "fas fa-chart-line",
"properties": {
"plotvar": {
"type": "string",
"default": "RICHNESS_ALL,PD,PD_P",
"fa_icon": "fas fa-chart-line",
"description": "Variables to plot (multiple comma-separated values allowed); e.g., \"RICHNESS_ALL,PD,PD_P\""
},
"plottype": {
"type": "string",
"default": "raw",
"fa_icon": "fas fa-chart-line",
"description": "Plot type"
},
"plotformat": {
"type": "string",
"default": "pdf",
"fa_icon": "fas fa-chart-line",
"description": "Plot format (jpg,pdf,png)",
"enum": ["pdf", "png", "jpg"]
},
"plotwidth": {
"type": "number",
"default": 18,
"fa_icon": "fas fa-chart-line",
"description": "Plot width (default, 18 inches)"
},
"plotheight": {
"type": "number",
"default": 18,
"fa_icon": "fas fa-chart-line",
"description": "Plot height (default, 18 inches)"
},
"plotunits": {
"type": "string",
"default": "in",
"fa_icon": "fas fa-chart-line",
"description": "Plot size units (in,cm)",
"enum": ["in", "cm", "px"]
},
"world": {
"type": "string",
"default": "params.data_path + \"/WorldMap_NaturalEarth_Medium.RData\"",
"fa_icon": "fas fa-chart-line",
"description": "World basemap"
}
}
},
"phylogenetic_tree_related_parameters": {
"title": "Phylogenetic tree-related parameters",
"type": "object",
"description": "",
"default": "",
"fa_icon": "fas fa-brain",
"properties": {
"taxgroup": {
"type": "string",
"default": "All_life",
"fa_icon": "fas fa-sitemap",
"description": "Specific taxonomy group in Open Tree of Life (default, \"All_life\")",
"enum": [
"All_life",
"Animals",
"Birds",
"Tetrapods",
"Mammals",
"Amphibians",
"Vertebrates",
"Arthropods",
"Molluscs",
"Nematodes",
"Platyhelminthes",
"Annelids",
"Cnidarians",
"Arachnids",
"Insects",
"Fungi",
"Basidiomycetes",
"Ascomycetes",
"Bacteria",
"SAR_group",
"Archaea",
"Excavata",
"Amoebozoa",
"Centrohelida",
"Haptophyta",
"Apusozoa",
"Diatoms",
"Ciliates",
"Forams",
"Land_plants",
"Hornworts",
"Mosses",
"Liverworts",
"Vascular_plants",
"Club_mosses",
"Ferns",
"Seed_plants",
"Flowering_plants",
"Monocots",
"Eudicots",
"Rosids",
"Asterids",
"Asterales",
"Asteraceae",
"Aster",
"Symphyotrichum",
"Campanulaceae",
"Lobelia"
]
},
"phylabels": {
"type": "string",
"default": "Latin",
"fa_icon": "fas fa-tags",
"description": "Type of tip labels on a phylogenetic tree (\"OTT\" or \"Latin\")",
"enum": ["Latin", "OTT"]
},
"phyloonly": {
"type": "boolean",
"fa_icon": "fas fa-info-circle",
"description": "Prune Open Tree tips for which there are no phylogenetic inputs"
},
"maxage": {
"type": "number",
"fa_icon": "fas fa-compress-alt",
"description": "Manually assign root age for a tree obtained from Open Tree of Life"
}
}
},
"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": {
"deriveddataset": {
"type": "boolean",
"default": true,
"description": "Export list of GBIF dataset keys for the filtered species occurrences. Could be used for citation and to preparation derived dataset. (default, true)",
"fa_icon": "fas fa-list-alt"
},
"helpMsg": {
"type": "boolean",
"fa_icon": "far fa-question-circle",
"description": "Display help text (pipeline)"
},
"help": {
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle"
},
"scripts_path": {
"type": "string",
"default": "${projectDir}/bin",
"hidden": true,
"fa_icon": "fas fa-database",
"format": "directory-path",
"description": "Directory with pipeline scripts (default, `~/.nextflow/assets/vmikk/phylonext/bin/`)/"
},
"data_path": {
"type": "string",
"default": "${projectDir}/pipeline_data",
"hidden": true,
"fa_icon": "fas fa-database",
"format": "directory-path",
"description": "Directory with the built-in pipeline data (default, `~/.nextflow/assets/vmikk/phylonext/pipeline_data/`)"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"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})$",
"help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"hidden": true
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"tracedir": {
"type": "string",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"default": "${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."
},
"enable_conda": {
"type": "boolean",
"description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
"fa_icon": "fas fa-bacon",
"hidden": true
}
}
},
"max_job_request_options": {
"title": "Max job request options",
"type": "object",
"fa_icon": "fas fa-user-md",
"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",
"help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`",
"hidden": true
},
"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$",
"help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`",
"hidden": true
},
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job.",
"default": "240.h",
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
"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'`",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/taxonomic_scope"
},
{
"$ref": "#/definitions/spatial_scope"
},
{
"$ref": "#/definitions/spatial_outliers_removal"
},
{
"$ref": "#/definitions/occurrence_filtering_and_binning"
},
{
"$ref": "#/definitions/coordinatecleaner_like_filtering"
},
{
"$ref": "#/definitions/biodeverse"
},
{
"$ref": "#/definitions/visualization_interactive"
},
{
"$ref": "#/definitions/visualization_static"
},
{
"$ref": "#/definitions/phylogenetic_tree_related_parameters"
},
{
"$ref": "#/definitions/generic_options"
},
{
"$ref": "#/definitions/max_job_request_options"
}
]
}