forked from nf-core/viralrecon
-
Notifications
You must be signed in to change notification settings - Fork 1
/
nextflow_schema.json
696 lines (696 loc) · 37.8 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
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/nf-core/viralrecon/master/nextflow_schema.json",
"title": "nf-core/viralrecon pipeline parameters",
"description": "Assembly and intrahost/low-frequency variant calling for viral samples",
"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.",
"properties": {
"input": {
"type": "string",
"format": "file-path",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"schema": "assets/schema_input.json",
"fa_icon": "fas fa-file-csv",
"help_text": "You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/viralrecon/docs/usage#introduction).",
"description": "Path to comma-separated file containing information about the samples you would like to analyse."
},
"platform": {
"type": "string",
"fa_icon": "fas fa-hdd",
"description": "NGS platform used to sequence the samples"
},
"protocol": {
"type": "string",
"description": "Specifies the type of protocol used for sequencing i.e. 'metagenomic' or 'amplicon'.",
"fa_icon": "fas fa-vials"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved.",
"default": "./results",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
}
}
},
"reference_genome_options": {
"title": "Reference genome options",
"type": "object",
"fa_icon": "fas fa-dna",
"description": "Options for the reference genome indices used to align reads.",
"properties": {
"genome": {
"type": "string",
"description": "Name of viral reference genome.",
"fa_icon": "fas fa-book",
"help_text": "You can find the keys to specify the genomes in the [Genomes config file](https://github.com/nf-core/configs/blob/master/conf/pipeline/viralrecon/genomes.config)."
},
"fasta": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "fas fa-font",
"description": "Path to FASTA genome file.",
"help_text": "If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible."
},
"gff": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.gff(\\.gz)?$",
"description": "Full path to GFF annotation file.",
"fa_icon": "fas fa-file-invoice"
},
"bowtie2_index": {
"type": "string",
"format": "path",
"description": "Path to directory or tar.gz archive for pre-built Bowtie2 index.",
"fa_icon": "fas fa-bezier-curve"
},
"primer_bed": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"description": "If the '--protocol amplicon' parameter is provided then iVar is used to trim primer sequences after read alignment and before variant calling.",
"help_text": "iVar uses the primer positions relative to the viral genome supplied in this file to soft clip primer sequences from a coordinate sorted BAM file. The file must be in BED format as highlighted below:\n\n```\nMN908947.3 30 54 nCoV-2019_1_LEFT 60 -\nMN908947.3 385 410 nCoV-2019_1_RIGHT 60 +\nMN908947.3 320 342 nCoV-2019_2_LEFT 60 -\nMN908947.3 704 726 nCoV-2019_2_RIGHT 60 +\n```",
"fa_icon": "fas fa-stream"
},
"primer_fasta": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"description": "If the '--protocol amplicon' parameter is provided then Cutadapt is used to trim primer sequences from FastQ files before de novo assembly.",
"help_text": "This file must contain amplicon primer sequences in Fasta format. An example is shown below:\n\n```\n>nCoV-2019_1_LEFT\nACCAACCAACTTTCGATCTCTTGT\n>nCoV-2019_1_RIGHT\nCATCTTTAAGATGTTGACGTGCCTC\n>nCoV-2019_2_LEFT\nCTGTTTTACAGGTTCGCGACGT\n>nCoV-2019_2_RIGHT\nTAAGGATCAGTGCCAAGCTCGT\n```",
"fa_icon": "fas fa-stream"
},
"primer_set": {
"type": "string",
"fa_icon": "fas fa-sliders-h",
"description": "The primer set to be used for the data analysis.",
"help_text": "Where possible we are trying to collate links and settings for standard primer sets to make it easier to run the pipeline with standard keys. See https://github.com/nf-core/configs/blob/master/conf/pipeline/viralrecon/genomes.config"
},
"primer_set_version": {
"type": "integer",
"fa_icon": "fas fa-code-branch",
"description": "Version of the primer set e.g. '--primer_set artic --primer_set_version 3'.",
"help_text": "Where possible we are trying to collate links and settings for standard primer sets to make it easier to run the pipeline with standard keys. See https://github.com/nf-core/configs/blob/master/conf/pipeline/viralrecon/genomes.config"
},
"primer_left_suffix": {
"type": "string",
"default": "_LEFT",
"fa_icon": "fas fa-arrow-left",
"description": "Suffix used in name field of '--primer_bed' to indicate left primer position."
},
"primer_right_suffix": {
"type": "string",
"default": "_RIGHT",
"fa_icon": "fas fa-arrow-right",
"description": "Suffix used in name field of '--primer_bed' to indicate right primer position."
},
"save_reference": {
"type": "boolean",
"fa_icon": "fas fa-save",
"description": "If generated by the pipeline save reference genome related files to the results folder."
}
}
},
"nanopore_options": {
"title": "Nanopore options",
"type": "object",
"description": "Options exclusive to running the pipeline on Nanopore data using the ARTIC fieldbioinformatics pipeline.",
"default": "",
"fa_icon": "fas fa-truck-loading",
"properties": {
"fastq_dir": {
"type": "string",
"format": "directory-path",
"description": "Path to a folder containing fastq files from the Nanopore run.",
"help_text": "e.g. '--fastq_dir ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/fastq_pass/'.",
"fa_icon": "fas fa-folder-open"
},
"fast5_dir": {
"type": "string",
"format": "directory-path",
"description": "Path to a folder containing fast5 files from the Nanopore run.",
"help_text": "e.g. '--fast5_dir ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/fast5_pass/'. Not required when running the pipeline with the '--artic_minion_caller medaka' workflow.",
"fa_icon": "fas fa-folder-open"
},
"sequencing_summary": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.txt$",
"description": "Sequencing summary file generated after Nanopore run completion.",
"help_text": " e.g. '--sequencing_summary ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/sequencing_summary.txt'. Not required when running the pipeline with the '--artic_minion_caller medaka' workflow.",
"fa_icon": "fas fa-file"
},
"min_barcode_reads": {
"type": "integer",
"default": 100,
"description": "Minimum number of raw reads required per sample/barcode in order to be considered for the downstream processing steps.",
"fa_icon": "fas fa-hand-paper"
},
"min_guppyplex_reads": {
"type": "integer",
"default": 10,
"description": "Minimum number of reads required after the artic guppyplex process per sample/barcode in order to be considered for the downstream processing steps.",
"fa_icon": "fas fa-hand-paper"
},
"artic_minion_caller": {
"type": "string",
"default": "nanopolish",
"description": "Variant caller used when running artic minion. Available options are 'medaka' and 'nanopolish' (default).",
"fa_icon": "fas fa-phone-volume"
},
"artic_minion_aligner": {
"type": "string",
"default": "minimap2",
"description": "Aligner used when running artic minion. Available options are 'bwa' and 'minimap2' (default).",
"fa_icon": "fas fa-map-signs"
},
"artic_scheme": {
"type": "string",
"description": "Primer scheme recognised by the artic minion command.",
"help_text": "e.g. '--artic_scheme ncov-2019'. See https://artic.readthedocs.io/en/latest/primer-schemes/ and https://github.com/artic-network/primer-schemes/blob/master/schemes_manifest.json.",
"fa_icon": "fas fa-stream"
},
"artic_minion_medaka_model": {
"type": "string",
"description": "Parameter passed to artic minion and required when using the '--artic_minion_caller medaka' workflow.",
"help_text": "See https://github.com/nanoporetech/medaka",
"fa_icon": "fas fa-train"
},
"skip_pycoqc": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip pycoQC."
},
"skip_nanoplot": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip NanoPlot."
}
}
},
"nanopore_illumina_options": {
"title": "Nanopore/Illumina options",
"type": "object",
"description": "Options common to both the Nanopore and Illumina workflows in the pipeline.",
"default": "",
"properties": {
"asciigenome_read_depth": {
"type": "integer",
"default": 50,
"description": "Maximum read depth used to generate ASCIIGenome screenshots for variant locii.",
"fa_icon": "fas fa-align-center"
},
"asciigenome_window_size": {
"type": "integer",
"default": 50,
"description": "Maximum window size before and after variant locii used to generate ASCIIGenome screenshots.",
"fa_icon": "fab fa-windows"
},
"multiqc_title": {
"type": "string",
"hidden": true,
"fa_icon": "fas fa-signature",
"description": "Custom title for the MultiQC report."
},
"multiqc_config": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"max_multiqc_email_size": {
"type": "string",
"description": "File size limit when attaching MultiQC reports to summary emails.",
"default": "25.MB",
"fa_icon": "fas fa-file-upload",
"hidden": true,
"help_text": "If file generated by pipeline exceeds the threshold, it will not be attached."
},
"skip_mosdepth": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip genome-wide and amplicon coverage plot generation from mosdepth output."
},
"skip_pangolin": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip Pangolin lineage analysis for genome consensus sequence."
},
"skip_nextclade": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip Nextclade clade assignment, mutation calling, and sequence quality checks for genome consensus sequence."
},
"skip_asciigenome": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip variant screenshot generation with ASCIIGenome."
},
"skip_variants_quast": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip generation of QUAST aggregated report for consensus sequences."
},
"skip_multiqc": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip MultiQC."
}
},
"fa_icon": "fas fa-retweet"
},
"illumina_qc_read_trimming_and_filtering_options": {
"title": "Illumina QC, read trimming and filtering options",
"type": "object",
"description": "Options to adjust QC, read trimming and host read filtering with Kraken2 for the Illumina workflow.",
"default": "",
"properties": {
"kraken2_db": {
"type": "string",
"format": "path",
"default": "s3://nf-core-awsmegatests/viralrecon/input_data/kraken2_human.tar.gz",
"fa_icon": "fab fa-gitkraken",
"description": "Full path to Kraken2 database built from host genome."
},
"kraken2_db_name": {
"type": "string",
"default": "human",
"fa_icon": "fab fa-gitkraken",
"description": "Name for host genome as recognised by Kraken2 when using the 'kraken2 build' command."
},
"kraken2_variants_host_filter": {
"type": "boolean",
"fa_icon": "fab fa-gitkraken",
"description": "Remove host reads identified by Kraken2 before running variant calling steps in the pipeline."
},
"kraken2_assembly_host_filter": {
"type": "boolean",
"default": true,
"fa_icon": "fab fa-gitkraken",
"description": "Remove host reads identified by Kraken2 before running aseembly steps in the pipeline."
},
"save_trimmed_fail": {
"type": "boolean",
"fa_icon": "fas fa-save",
"description": "Save the trimmed FastQ files in the results directory.",
"help_text": "By default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete."
},
"skip_fastqc": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip FastQC."
},
"skip_kraken2": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip Kraken2 process for removing host classified reads."
},
"skip_fastp": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip the initial read trimming step peformed by fastp."
},
"skip_cutadapt": {
"type": "boolean",
"description": "Skip the amplicon trimming step with Cutadapt when using --protocol amplicon.",
"fa_icon": "fas fa-fast-forward"
}
},
"fa_icon": "fas fa-cut"
},
"illumina_variant_calling_options": {
"title": "Illumina variant calling options",
"type": "object",
"description": "Various options for the variant calling branch of the Illumina workflow.",
"default": "",
"properties": {
"callers": {
"type": "string",
"description": "Specify which variant calling algorithms you would like to use. Available options are 'ivar' (default for '--protocol amplicon') and 'bcftools' (default for '--protocol metagenomic').",
"fa_icon": "fas fa-phone-volume"
},
"min_mapped_reads": {
"type": "integer",
"default": 1000,
"description": "Minimum number of mapped reads below which samples are removed from further processing. Some downstream steps in the pipeline will fail if this threshold is too low.",
"fa_icon": "fas fa-hand-paper"
},
"ivar_trim_noprimer": {
"type": "boolean",
"description": "This option unsets the '-e' parameter in 'ivar trim' to discard reads without primers.",
"fa_icon": "fas fa-cut"
},
"ivar_trim_offset": {
"type": "integer",
"description": "This option sets the '-x' parameter in 'ivar trim' so that reads that occur at the specified offset positions relative to primer positions will also be trimmed.",
"fa_icon": "fas fa-cut",
"help_text": "This parameter will need to be set for some amplicon-based sequencing protocols (e.g. SWIFT) as described and implemented [here](https://github.com/andersen-lab/ivar/pull/88)"
},
"filter_duplicates": {
"type": "boolean",
"fa_icon": "fas fa-clone",
"description": "Filtered duplicates reads detected by Picard MarkDuplicates from alignments."
},
"save_unaligned": {
"type": "boolean",
"fa_icon": "fas fa-save",
"description": "Save unaligned reads in FastQ format from Bowtie 2 to the results directory."
},
"save_mpileup": {
"type": "boolean",
"fa_icon": "fas fa-save",
"description": "Save mpileup files generated when calling variants with iVar variants or iVar consensus."
},
"skip_ivar_trim": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip iVar primer trimming step. Not recommended for --protocol amplicon."
},
"skip_markduplicates": {
"type": "boolean",
"default": true,
"fa_icon": "fas fa-fast-forward",
"description": "Skip picard MarkDuplicates step."
},
"skip_picard_metrics": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip Picard CollectMultipleMetrics steps."
},
"skip_snpeff": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip SnpEff and SnpSift annotation of variants."
},
"skip_consensus": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip genome consensus creation step and any downstream QC."
},
"skip_variants": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Specify this parameter to skip all of the variant calling and mapping steps in the pipeline."
}
},
"fa_icon": "fas fa-dna"
},
"illumina_de_novo_assembly_options": {
"title": "Illumina de novo assembly options",
"type": "object",
"description": "Various options for the de novo assembly branch of the Illumina workflow.",
"default": "",
"properties": {
"assemblers": {
"type": "string",
"default": "spades",
"description": "Specify which assembly algorithms you would like to use. Available options are 'spades', 'unicycler' and 'minia'.",
"fa_icon": "fas fa-random"
},
"spades_mode": {
"type": "string",
"default": "rnaviral",
"fa_icon": "fab fa-digg",
"description": "Specify the SPAdes mode you would like to run. Supported options are 'rnaviral', 'corona', 'metaviral', 'meta', 'metaplasmid', 'plasmid', 'isolate', 'rna', 'bio'."
},
"spades_hmm": {
"type": "string",
"format": "file-path",
"fa_icon": "fab fa-digg",
"description": "Path to profile HMMs specific for gene/organism to enhance SPAdes assembly."
},
"blast_db": {
"type": "string",
"format": "path",
"fa_icon": "fas fa-database",
"description": "Path to directory or tar.gz archive for pre-built BLAST database."
},
"skip_bandage": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip Bandage image creation for assembly visualisation."
},
"skip_blast": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip blastn of assemblies relative to reference genome."
},
"skip_abacas": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip ABACAS process for assembly contiguation."
},
"skip_plasmidid": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip assembly report generation by PlasmidID."
},
"skip_assembly_quast": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Skip generation of QUAST aggregated report for assemblies."
},
"skip_assembly": {
"type": "boolean",
"fa_icon": "fas fa-fast-forward",
"description": "Specify this parameter to skip all of the de novo assembly steps in the pipeline."
}
},
"fa_icon": "fas fa-random"
},
"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.",
"hidden": true,
"fa_icon": "fas fa-question-circle"
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"hidden": true,
"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})$",
"hidden": true,
"help_text": "This works exactly as with `--email`, except emails are only sent if the workflow is not successful."
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true,
"help_text": "Set to receive plain-text e-mails instead of HTML formatted."
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true,
"help_text": "Set to disable colourful command line output and live life in monochrome."
},
"tracedir": {
"type": "string",
"format": "directory-path",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"default": "${params.outdir}/pipeline_info",
"fa_icon": "fas fa-cogs",
"hidden": true
},
"enable_conda": {
"type": "boolean",
"hidden": true,
"description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
"fa_icon": "fas fa-bacon"
},
"singularity_pull_docker_container": {
"type": "boolean",
"hidden": true,
"description": "Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.",
"fa_icon": "fas fa-toolbox",
"help_text": "This may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues."
},
"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."
}
}
},
"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'`"
}
}
},
"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",
"help_text": "Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default: `master`.\n\n```bash\n## Download and use config file with following git commit id\n--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96\n```"
},
"custom_config_base": {
"type": "string",
"format": "directory-path",
"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 the `custom_config_base` option. For example:\n\n```bash\n## Download and unzip the config files\ncd /path/to/my/configs\nwget https://github.com/nf-core/configs/archive/master.zip\nunzip master.zip\n\n## Run the pipeline\ncd /path/to/my/data\nnextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/\n```\n\n> Note that the nf-core/tools helper package has a `download` command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.",
"fa_icon": "fas fa-users-cog"
},
"hostnames": {
"type": "string",
"description": "Institutional configs hostname.",
"hidden": true,
"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"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/reference_genome_options"
},
{
"$ref": "#/definitions/nanopore_options"
},
{
"$ref": "#/definitions/nanopore_illumina_options"
},
{
"$ref": "#/definitions/illumina_qc_read_trimming_and_filtering_options"
},
{
"$ref": "#/definitions/illumina_variant_calling_options"
},
{
"$ref": "#/definitions/illumina_de_novo_assembly_options"
},
{
"$ref": "#/definitions/generic_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/institutional_config_options"
}
]
}