forked from WangLab-ComputationalBiology/btc-scrna-pipeline
-
Notifications
You must be signed in to change notification settings - Fork 5
/
nextflow_schema.json
509 lines (509 loc) · 21.3 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
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/nf-core/test/master/nextflow_schema.json",
"title": "nf-core/test pipeline parameters",
"description": "BTC scRNA Pipeline",
"type": "object",
"definitions": {
"pipeline_parameters": {
"title": "Pipeline parameters",
"type": "object",
"description": "Parameters related to data flow",
"properties": {
"workflow_level": {
"type": "string",
"default": "Complete",
"description": "Defining the pipeline entrypoint"
},
"skip_deg": {
"type": "boolean",
"description": "Skipping Differential expression analysis"
},
"skip_com": {
"type": "boolean",
"description": "Skipping Cell-cell communication analysis"
},
"skip_dbl": {
"type": "boolean",
"description": "Skipping Doublet detection analysis"
}
}
},
"project_parameters": {
"title": "Project parameters",
"type": "object",
"fa_icon": "fas fa-dna",
"description": "Reference genome related files and options required for the workflow.",
"properties": {
"sample_table": {
"type": "string",
"default": "./assets/test_sample_table.csv",
"description": "Path to sample table"
},
"meta_data": {
"type": "string",
"default": "./assets/test_meta_data.csv",
"fa_icon": "fas fa-address-card",
"description": "Path to meta-data"
},
"project_name": {
"type": "string",
"default": "Test",
"description": "Project name"
},
"cancer_type": {
"type": "string",
"default": "None",
"description": "Enter the cancer type"
},
"igenomes_base": {
"type": "string",
"default": "gs://btc-refdata/scRNA/refData",
"description": "Enter URL/Path to the genome"
},
"genome": {
"type": "string",
"description": "Genome ID",
"fa_icon": "fas fa-book",
"help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.",
"default": "GRCh38"
},
"fasta": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"description": "Path to FASTA genome file.",
"help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
"fa_icon": "far fa-file-code"
}
}
},
"quality_control_parameters": {
"title": "Quality Control parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"thr_estimate_n_cells": {
"type": "integer",
"default": 300,
"description": "Estimated number of cells"
},
"thr_mean_reads_per_cells": {
"type": "integer",
"default": 25000,
"description": "Mean reads per cell"
},
"thr_median_genes_per_cell": {
"type": "integer",
"default": 900,
"description": "Median genes per cell"
},
"thr_median_umi_per_cell": {
"type": "integer",
"default": 1000,
"description": "Median UMI per cell"
},
"thr_n_feature_rna_min": {
"type": "integer",
"default": 300,
"description": "Minimum features per cell"
},
"thr_n_feature_rna_max": {
"type": "integer",
"default": 7500,
"description": "Maximum features per cell"
},
"thr_percent_mito": {
"type": "integer",
"default": 25,
"description": "Percentage of mitochondrial genes"
},
"thr_n_observed_cells": {
"type": "integer",
"default": 300,
"description": "Number of observed cells"
}
}
},
"normalization_parameters": {
"title": "Normalization parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"input_reduction_step": {
"type": "string",
"default": "None",
"description": "Internal pipeline parameter. Do not customize it.",
"hidden": true
},
"thr_n_features": {
"type": "integer",
"default": 2000,
"description": "Number features for FindVariableFeatures"
}
}
},
"clustering_parameters": {
"title": "Clustering parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"input_cluster_step": {
"type": "string",
"default": "None",
"description": "Internal pipeline parameter. Do not customize it.",
"hidden": true
},
"input_features_plot": {
"type": "string",
"default": "LYZ;CCL5;IL32;PTPRCAP;FCGR3A;PF4;PTPRC",
"description": "Genes to be displayed on Feature plot"
},
"input_integration_dimension": {
"type": "string",
"default": "auto",
"description": "Embeddings for Louvain clustering"
},
"input_group_plot": {
"type": "string",
"default": "source_name;Sort",
"description": "Meta-data columns for UMAP plot"
},
"thr_resolution": {
"type": "number",
"default": 0.25,
"description": "Resolution threshold"
},
"thr_proportion": {
"type": "number",
"default": 0.25,
"description": "Cell proportion for ROGUE calculation"
}
}
},
"stratification_parameters": {
"title": "Stratification parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"input_stratification_method": {
"type": "string",
"default": "infercnv_label",
"description": "Method to define stratification labels"
},
"thr_cluster_size": {
"type": "integer",
"default": 1000,
"description": "Defining cluster size limit"
},
"thr_consensus_score": {
"type": "integer",
"default": 2,
"description": "Consensus score threshold (Beta)"
}
}
},
"cell_annotations_parameters": {
"title": "Cell annotations parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"input_cell_markers_db": {
"type": "string",
"default": "./assets/cell_markers_database.csv",
"description": "Path to cell annotation CSV file"
},
"input_annotation_level": {
"type": "string",
"default": "Major cells",
"description": "Define annotation level. Currently, only Major cells are available."
}
}
},
"cell_communication_parameters": {
"title": "Cell-cell communication parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"input_source_groups": {
"type": "string",
"default": "all",
"description": "Source cell type names"
},
"input_target_groups": {
"type": "string",
"default": "all",
"description": "Target cell type names"
},
"input_cellchat_annotation": {
"type": "string",
"default": "Secreted Signaling",
"description": "CellChat interactions type"
}
}
},
"batch_correction_parameters": {
"title": "Batch correction parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"input_batch_step": {
"type": "string",
"default": "None",
"description": "Internal pipeline parameter. Do not customize it.",
"hidden": true
},
"input_integration_method": {
"type": "string",
"default": "all",
"description": "Batch correction / Integration methods. Default (all)."
},
"input_target_variables": {
"type": "string",
"default": "batch",
"description": "Meta-data target variable for batch correction"
}
}
},
"batch_evaluation_parameters": {
"title": "Batch Evaluation parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"input_integration_evaluate": {
"type": "string",
"default": "all",
"description": "Define methods to be evaluated"
},
"thr_cell_proportion": {
"type": "number",
"default": 0.3,
"description": "Cell proportion for Batch evaluation"
},
"input_lisi_variables": {
"type": "string",
"default": "cLISI;iLISI",
"description": "Define LISI types for Density plot"
},
"input_auto_selection": {
"type": "boolean",
"default": true,
"hidden": true,
"description": "Internal pipeline parameter. Do not customize it."
}
}
},
"differential_expression_parameters": {
"title": "Differential Expression parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"input_deg_step": {
"type": "string",
"default": "None",
"description": "Internal pipeline parameter. Do not customize it.",
"hidden": true
},
"input_deg_method": {
"type": "string",
"default": "wilcox",
"description": "Define DEG method (check options at Seurat documentation)"
},
"input_top_deg": {
"type": "integer",
"default": 20,
"description": "Number of DEG to be displayed"
},
"thr_fold_change": {
"type": "number",
"default": 0.25,
"description": "Fold-change threshold"
},
"thr_min_percentage": {
"type": "number",
"default": 0.1,
"description": "Minimum cell percentage per DEG"
},
"opt_hgv_filter": {
"type": "boolean",
"description": "Filtering only HGV genes (Optional)"
}
}
},
"meta_program_parameters": {
"title": "Meta-program parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"input_meta_step": {
"type": "string",
"default": "None",
"description": "Internal pipeline parameter. Do not customize it.",
"hidden": true
},
"input_meta_programs_db": {
"type": "string",
"default": "./assets/meta_programs_database.csv",
"description": "Path to meta-program CSV file"
},
"input_cell_category": {
"type": "string",
"default": "Malignant",
"description": "Meta-program cell category"
},
"input_heatmap_annotation": {
"type": "string",
"default": "source_name;seurat_clusters",
"description": "Meta-data columns to be displayed on heatmap"
}
}
},
"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*)+$",
"hidden": true,
"help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"help": {
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"tracedir": {
"type": "string",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"default": "${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."
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/pipeline_parameters"
},
{
"$ref": "#/definitions/project_parameters"
},
{
"$ref": "#/definitions/quality_control_parameters"
},
{
"$ref": "#/definitions/normalization_parameters"
},
{
"$ref": "#/definitions/clustering_parameters"
},
{
"$ref": "#/definitions/stratification_parameters"
},
{
"$ref": "#/definitions/cell_annotations_parameters"
},
{
"$ref": "#/definitions/cell_communication_parameters"
},
{
"$ref": "#/definitions/batch_correction_parameters"
},
{
"$ref": "#/definitions/batch_evaluation_parameters"
},
{
"$ref": "#/definitions/differential_expression_parameters"
},
{
"$ref": "#/definitions/meta_program_parameters"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/generic_options"
}
]
}