-
Notifications
You must be signed in to change notification settings - Fork 1
/
nextflow_schema.json
667 lines (667 loc) · 32.7 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
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/nf-cmgg/germline/master/nextflow_schema.json",
"title": "nf-cmgg/germline pipeline parameters",
"description": "A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data",
"type": "object",
"$defs": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.(csv|tsv|yaml|yml|json)$",
"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 samples, and a header row. See [usage docs](./usage.md).",
"fa_icon": "fas fa-file-csv",
"mimetype": "text/plain"
},
"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"
},
"watchdir": {
"type": "string",
"format": "directory-path",
"description": "A folder to watch for the creation of files that start with `watch:` in the samplesheet",
"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})$"
},
"ped": {
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.ped$",
"description": "Path to a pedigree file for all samples in the run"
}
}
},
"reference_genome_options": {
"title": "Reference genome options",
"type": "object",
"fa_icon": "fas fa-dna",
"description": "Reference genome related files and options required for the workflow.",
"properties": {
"genome": {
"type": "string",
"default": "GRCh38",
"description": "Reference genome build",
"help_text": "Requires a Genome Reference Consortium reference ID (e.g. GRCh38)"
},
"fasta": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?$",
"description": "Path to FASTA genome file.",
"help_text": "This parameter is *mandatory* if `--genome` is not specified. The path to the reference genome fasta.",
"fa_icon": "far fa-file-code"
},
"fai": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fai$",
"description": "Path to FASTA genome index file.",
"fa_icon": "far fa-file-code"
},
"dict": {
"type": "string",
"pattern": "^\\S+\\.dict$",
"description": "Path to the sequence dictionary generated from the FASTA reference",
"fa_icon": "far fa-file-code",
"format": "file-path",
"mimetype": "text/plain"
},
"strtablefile": {
"type": "string",
"description": "Path to the STR table file generated from the FASTA reference",
"fa_icon": "fas fa-folder",
"format": "path"
},
"sdf": {
"type": "string",
"description": "Path to the SDF folder generated from the reference FASTA file",
"format": "path",
"fa_icon": "fas fa-folder"
},
"genomes_base": {
"type": "string",
"default": "/references/",
"description": "Directory base for CMGG reference store (used when --genomes_ignore false is specified)",
"fa_icon": "fas fa-download",
"format": "directory-path"
},
"cmgg_config_base": {
"type": "string",
"default": "/conf/",
"description": "The base directory for the local config files",
"fa_icon": "fas fa-folder",
"hidden": true
},
"genomes_ignore": {
"type": "boolean",
"hidden": true,
"description": "Do not load the local references from the path specified with --genomes_base",
"fa_icon": "fas fa-ban"
},
"igenomes_base": {
"type": "string",
"format": "directory-path",
"description": "Directory / URL base for iGenomes references.",
"fa_icon": "fas fa-cloud-download-alt",
"hidden": true
},
"igenomes_ignore": {
"type": "boolean",
"description": "Do not load the iGenomes reference config.",
"fa_icon": "fas fa-ban",
"hidden": true,
"help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
}
},
"required": ["fasta"]
},
"pipeline_specific_parameters": {
"title": "Pipeline specific parameters",
"type": "object",
"description": "Parameters that define how the pipeline works",
"default": "",
"properties": {
"scatter_count": {
"type": "integer",
"default": 40,
"description": "The amount of scattering that should happen per sample.",
"help_text": "Increase this number to increase the pipeline run speed, but at the tradeoff of using more IO and disk space. This can differ from the actual scatter count in some cases (especially with smaller files).\nThis has an effect on HaplotypeCaller, GenomicsDBImport and GenotypeGVCFs.",
"minimum": 1
},
"merge_distance": {
"type": "integer",
"default": 100000,
"description": "The merge distance for genotype BED files",
"help_text": "Increase this parameter if GenomicsDBImport is running slow. This defines the maximum distance between intervals that should be merged. The less intervals GenomicsDBImport actually gets, the faster it will run."
},
"dragstr": {
"type": "boolean",
"description": "Create DragSTR models to be used with HaplotypeCaller",
"help_text": "This currently is only able to run single-core per sample. Due to this, the process is very slow with only very small improvements to the analysis."
},
"validate": {
"type": "boolean",
"description": "Validate the found variants",
"help_text": "This only validates individual sample GVCFs that have truth VCF supplied to them via the samplesheet (in row `truth_vcf`, with an optional index in the `truth_tbi` row)"
},
"filter": {
"type": "boolean",
"description": "Filter the found variants"
},
"annotate": {
"type": "boolean",
"description": "Annotate the found variants"
},
"add_ped": {
"type": "boolean",
"description": "Add PED INFO header lines to the final VCFs"
},
"gemini": {
"type": "boolean",
"description": "Create a Gemini databases from the final VCFs"
},
"mosdepth_slow": {
"type": "boolean",
"description": "Don't run mosdepth in fast-mode",
"help_text": "This is advised if you need exact coverage BED files as output"
},
"project": {
"type": "string",
"description": "The name of the project.",
"help_text": "This will be used to specify the final output files folder in the output directory."
},
"skip_date_project": {
"type": "boolean",
"description": "Don't add the current date to the output project folder"
},
"roi": {
"type": "string",
"description": "Path to the default ROI (regions of interest) BED file to be used for WES analysis",
"help_text": "This will be used for all samples that do not have a specific ROI file supplied to them through the samplesheet. Don't supply an ROI file to run the analysis as WGS.",
"format": "file-path",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"mimetype": "text/plain"
},
"dbsnp": {
"type": "string",
"description": "Path to the dbSNP VCF file",
"fa_icon": "far fa-file-alt",
"format": "file-path",
"pattern": "^\\S+\\.vcf\\.gz$",
"mimetype": "text/plain"
},
"dbsnp_tbi": {
"type": "string",
"description": "Path to the index of the dbSNP VCF file",
"fa_icon": "far fa-file-alt",
"format": "file-path",
"pattern": "^\\S+\\.tbi$",
"mimetype": "text/plain"
},
"somalier_sites": {
"type": "string",
"default": "https://github.com/brentp/somalier/files/3412456/sites.hg38.vcf.gz",
"fa_icon": "far fa-file-alt",
"description": "Path to the VCF file with sites for Somalier to use",
"pattern": "^\\S+\\.vcf\\.gz",
"format": "file-path",
"mimetype": "text/plain"
},
"only_call": {
"type": "boolean",
"description": "Only call the variants without doing any post-processing"
},
"only_merge": {
"type": "boolean",
"description": "Only run the pipeline until the creation of the genomicsdbs and output them"
},
"output_genomicsdb": {
"type": "boolean",
"description": "Output the genomicsDB together with the joint-genotyped VCF"
},
"callers": {
"type": "string",
"description": "A comma delimited string of the available callers. Current options are: 'haplotypecaller' and 'vardict'",
"default": "haplotypecaller"
},
"vardict_min_af": {
"type": "number",
"description": "The minimum allele frequency for VarDict when no `vardict_min_af` is supplied in the samplesheet",
"default": 0.1
},
"normalize": {
"type": "boolean",
"description": "Normalize the VCFs"
},
"output_suffix": {
"type": "string",
"description": "A custom suffix to add to the basename of the output files"
},
"only_pass": {
"type": "boolean",
"description": "Filter out all variants that don't have the PASS filter for vardict. This only works when --filter is also given"
},
"keep_alt_contigs": {
"type": "boolean",
"description": "Keep all aditional contigs for calling instead of filtering them out before"
},
"updio": {
"type": "boolean",
"description": "Run UPDio analysis on the resulting VCFs"
},
"updio_common_cnvs": {
"type": "string",
"description": "A TSV file containing common CNVs to be used by UPDio",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.tsv$"
},
"automap": {
"type": "boolean",
"description": "Run AutoMap analysis on the resulting VCFs"
},
"automap_repeats": {
"type": "string",
"description": "BED file with repeat regions in the genome.",
"help_text": "This file will be automatically generated for hg38/GRCh38 and hg19/GRCh37 when this parameter has not been given.",
"pattern": "^\\S+\\.bed$"
},
"automap_panel": {
"type": "string",
"description": "TXT file with gene panel regions to be used by AutoMap.",
"help_text": "By default the CMGG gene panel list will be used.",
"pattern": "^\\S+\\.txt$"
},
"automap_panel_name": {
"type": "string",
"default": "cmgg_bio",
"description": "The panel name of the panel given with --automap_panel."
},
"hc_phasing": {
"type": "boolean",
"description": "Perform phasing with HaplotypeCaller"
}
}
},
"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"
}
}
},
"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"
},
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle"
},
"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"]
},
"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."
},
"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"
},
"multiqc_config": {
"type": "string",
"format": "file-path",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog"
},
"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"
},
"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
},
"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
}
}
},
"annotation_parameters": {
"title": "Annotation parameters",
"type": "object",
"description": "Parameters to configure Ensembl VEP and VCFanno",
"default": "",
"properties": {
"vep_chunk_size": {
"type": "integer",
"default": 50000,
"description": "The amount of sites per split VCF as input to VEP"
},
"species": {
"type": "string",
"default": "homo_sapiens",
"description": "The species of the samples",
"fa_icon": "fas fa-user-circle",
"pattern": "^[a-z_]*$",
"help_text": "Must be lower case and have underscores as spaces"
},
"vep_merged": {
"type": "boolean",
"default": true,
"description": "Specify if the VEP cache is a merged cache"
},
"vep_cache": {
"type": "string",
"description": "The path to the VEP cache",
"format": "path"
},
"vep_dbnsfp": {
"type": "boolean",
"description": "Use the dbNSFP plugin with Ensembl VEP",
"fa_icon": "fas fa-question-circle",
"help_text": "The '--dbnsfp' and '--dbnsfp_tbi' parameters need to be specified when using this parameter."
},
"vep_spliceai": {
"type": "boolean",
"description": "Use the SpliceAI plugin with Ensembl VEP",
"fa_icon": "fas fa-question-circle",
"help_text": "The '--spliceai_indel', '--spliceai_indel_tbi', '--spliceai_snv' and '--spliceai_snv_tbi' parameters need to be specified when using this parameter."
},
"vep_spliceregion": {
"type": "boolean",
"description": "Use the SpliceRegion plugin with Ensembl VEP",
"fa_icon": "fas fa-question-circle"
},
"vep_mastermind": {
"type": "boolean",
"description": "Use the Mastermind plugin with Ensembl VEP",
"fa_icon": "fas fa-question-circle",
"help_text": "The '--mastermind' and '--mastermind_tbi' parameters need to be specified when using this parameter."
},
"vep_maxentscan": {
"type": "boolean",
"description": "Use the MaxEntScan plugin with Ensembl VEP",
"fa_icon": "fas fa-question-circle",
"help_text": "The '--maxentscan' parameter need to be specified when using this parameter."
},
"vep_eog": {
"type": "boolean",
"description": "Use the custom EOG annotation with Ensembl VEP",
"fa_icon": "fas fa-question-circle",
"help_text": "The '--eog' and '--eog_tbi' parameters need to be specified when using this parameter."
},
"vep_alphamissense": {
"type": "boolean",
"description": "Use the AlphaMissense plugin with Ensembl VEP",
"fa_icon": "fas fa-question-circle",
"help_text": "The '--alphamissense' and '--alphamissense_tbi' parameters need to be specified when using this parameter."
},
"vep_version": {
"type": "number",
"default": 105.0,
"description": "The version of the VEP tool to be used",
"fa_icon": "fas fa-code-branch"
},
"vep_cache_version": {
"type": "integer",
"default": 105,
"description": "The version of the VEP cache to be used",
"fa_icon": "fas fa-code-branch"
},
"dbnsfp": {
"type": "string",
"description": "Path to the dbSNFP file",
"format": "file-path",
"fa_icon": "far fa-file-alt",
"mimetype": "text/plain",
"pattern": "^\\S+\\.gz$"
},
"dbnsfp_tbi": {
"type": "string",
"format": "file-path",
"description": "Path to the index of the dbSNFP file",
"fa_icon": "far fa-file-alt",
"pattern": "^\\S+\\.(csi|tbi)$",
"mimetype": "text/plain"
},
"spliceai_indel": {
"type": "string",
"format": "file-path",
"description": "Path to the VCF containing indels for spliceAI",
"fa_icon": "far fa-file-alt",
"pattern": "^\\S+\\.vcf\\.gz$",
"mimetype": "text/plain"
},
"spliceai_indel_tbi": {
"type": "string",
"format": "file-path",
"description": "Path to the index of the VCF containing indels for spliceAI",
"pattern": "^\\S+\\.(csi|tbi)$",
"mimetype": "text/plain"
},
"spliceai_snv": {
"type": "string",
"format": "file-path",
"description": "Path to the VCF containing SNVs for spliceAI",
"pattern": "^\\S+\\.vcf\\.gz$",
"mimetype": "text/plain"
},
"spliceai_snv_tbi": {
"type": "string",
"format": "file-path",
"description": "Path to the index of the VCF containing SNVs for spliceAI",
"pattern": "^\\S+\\.(csi|tbi)$",
"mimetype": "text/plain"
},
"mastermind": {
"type": "string",
"format": "file-path",
"description": "Path to the VCF for Mastermind",
"pattern": "^\\S+\\.vcf\\.gz$",
"mimetype": "text/plain"
},
"mastermind_tbi": {
"type": "string",
"format": "file-path",
"description": "Path to the index of the VCF for Mastermind",
"pattern": "^\\S+\\.(csi|tbi)$",
"mimetype": "text/plain"
},
"alphamissense": {
"type": "string",
"format": "file-path",
"description": "Path to the TSV for AlphaMissense",
"pattern": "^\\S+\\.tsv\\.gz$",
"mimetype": "text/plain"
},
"alphamissense_tbi": {
"type": "string",
"format": "file-path",
"description": "Path to the index of the TSV for AlphaMissense",
"pattern": "^\\S+\\.(csi|tbi)$",
"mimetype": "text/plain"
},
"eog": {
"type": "string",
"format": "file-path",
"description": "Path to the VCF containing EOG annotations",
"pattern": "^\\S+\\.vcf\\.gz$",
"mimetype": "text/plain"
},
"eog_tbi": {
"type": "string",
"format": "file-path",
"description": "Path to the index of the VCF containing EOG annotations",
"pattern": "^\\S+\\.(csi|tbi)$",
"mimetype": "text/plain"
},
"vcfanno": {
"type": "boolean",
"description": "Run annotations with vcfanno"
},
"vcfanno_config": {
"type": "string",
"description": "The path to the VCFanno config TOML",
"pattern": "^\\S+\\.toml$",
"format": "file-path",
"mimetype": "text/plain"
},
"vcfanno_lua": {
"type": "string",
"description": "The path to a Lua script to be used in VCFanno",
"pattern": "^\\S+\\.lua$",
"format": "file-path",
"mimetype": "text/plain"
},
"vcfanno_resources": {
"type": "string",
"description": "A semicolon-seperated list of resource files for VCFanno, please also supply their indices using this parameter"
}
},
"help_text": "Annotation will only run when `--annotate true` is specified."
}
},
"allOf": [
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/reference_genome_options"
},
{
"$ref": "#/$defs/pipeline_specific_parameters"
},
{
"$ref": "#/$defs/institutional_config_options"
},
{
"$ref": "#/$defs/generic_options"
},
{
"$ref": "#/$defs/annotation_parameters"
}
]
}