forked from nf-core/proteinfold
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathnextflow.config
474 lines (432 loc) · 18.7 KB
/
nextflow.config
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
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/proteinfold Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
mode = 'alphafold2' // {alphafold2, colabfold, esmfold, rosettafold_all_atom, helixfold3}
use_gpu = false
split_fasta = false
// Alphafold2 parameters
alphafold2_mode = "standard"
max_template_date = "2020-05-14"
full_dbs = false // true full_dbs, false reduced_dbs
alphafold2_model_preset = "monomer" // for AF2 {monomer (default), monomer_casp14, monomer_ptm, multimer}
alphafold2_db = null
// Alphafold2 links
bfd_link = null
small_bfd_link = null
alphafold2_params_link = null
mgnify_link = null
pdb70_link = null
pdb_mmcif_link = null
pdb_obsolete_link = null
uniref30_alphafold2_link = null
uniref90_link = null
pdb_seqres_link = null
uniprot_sprot_link = null
uniprot_trembl_link = null
// Alphafold2 paths
bfd_path = null
small_bfd_path = null
alphafold2_params_path = null
mgnify_path = null
pdb70_path = null
pdb_mmcif_path = null
pdb_obsolete_path = null
uniref30_alphafold2_path = null
uniref90_path = null
pdb_seqres_path = null
uniprot_path = null
// Colabfold parameters
colabfold_server = "webserver"
colabfold_model_preset = "alphafold2_ptm" // {'auto', 'alphafold2', 'alphafold2_ptm', 'alphafold2_multimer_v1', 'alphafold2_multimer_v2', 'alphafold2_multimer_v3'}
num_recycles_colabfold = 3
use_amber = true
colabfold_db = null
db_load_mode = 0
host_url = null
use_templates = true
create_colabfold_index = false
// Colabfold links
colabfold_db_link = null
uniref30_colabfold_link = null
// Colabfold paths
colabfold_db_path = null
uniref30_colabfold_path = null
// Esmfold parameters
esmfold_db = null
esmfold_model_preset = "monomer"
num_recycles_esmfold = 4
// Esmfold links
esmfold_3B_v1 = null
esm2_t36_3B_UR50D = null
esm2_t36_3B_UR50D_contact_regression = null
// Esmfold paths
esmfold_params_path = null
// RoseTTAFold_All_Atom parameters
rosettafold_all_atom_db = null
// RoseTTAFold_All_Atom links
uniref30_rosettafold_all_atom_link = null
pdb100_rosettafold_all_atom_link = null
bfd_rosettafold_all_atom_path = null
rfaa_paper_weights_link = null
// RoseTTAFold_All_Atom paths
uniref30_rosettafold_all_atom_path = null
pdb100_rosettafold_all_atom_path = null
bfd_rosettafold_all_atom_path = null
rfaa_paper_weights_path = null
// Helixfold3 parameters
helixfold3_db = null
// Helixfold3 links
helixfold3_uniclust30_link = null
helixfold3_ccd_preprocessed_link = null
helixfold3_rfam_link = null
helixfold3_init_models_link = null
helixfold3_bfd_link = null
helixfold3_small_bfd_link = null
helixfold3_uniprot_sprot_link = null
helixfold3_uniprot_trembl_link = null
helixfold3_pdb_seqres_link = null
helixfold3_uniref90_link = null
helixfold3_mgnify_link = null
helixfold3_pdb_mmcif_link = null
helixfold3_pdb_obsolete_link = null
// Helixfold3 paths
helixfold3_uniclust30_path = null
helixfold3_ccd_preprocessed_path = null
helixfold3_rfam_path = null
helixfold3_init_models_path = null
helixfold3_bfd_path = null
helixfold3_small_bfd_path = null
helixfold3_uniprot_path = null
helixfold3_pdb_seqres_path = null
helixfold3_uniref90_path = null
helixfold3_mgnify_path = null
helixfold3_pdb_mmcif_path = null
helixfold3_maxit_src_path = null
// Foldseek params
foldseek_search = null
foldseek_easysearch_arg = null
// Process skipping options
skip_multiqc = false
skip_visualisation = false
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
help_full = false
show_hidden = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Schema validation default options
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.channels = ['conda-forge', 'bioconda']
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
if (params.use_gpu) {
docker.runOptions = '--gpus all'
} else {
docker.runOptions = '-u $(id -u):$(id -g)'
}
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
arm {
if (params.use_gpu) {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64 --gpus all'
} else {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
if (params.use_gpu) { singularity.runOptions = '--nv' }
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
if (params.use_gpu) { apptainer.runOptions = '--nv' }
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
wave {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
wave.enabled = true
wave.freeze = true
wave.strategy = 'conda,container'
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
process {
resourceLimits = [
memory: 8.GB,
cpus : 4,
time : 1.h
]
}
}
test { includeConfig 'conf/test.config' }
test_alphafold2_split { includeConfig 'conf/test_alphafold_split.config' }
test_alphafold2_download { includeConfig 'conf/test_alphafold_download.config' }
test_colabfold_local { includeConfig 'conf/test_colabfold_local.config' }
test_colabfold_webserver { includeConfig 'conf/test_colabfold_webserver.config' }
test_colabfold_download { includeConfig 'conf/test_colabfold_download.config' }
test_esmfold { includeConfig 'conf/test_esmfold.config' }
test_split_fasta { includeConfig 'conf/test_split_fasta.config' }
test_full { includeConfig 'conf/test_full.config' }
test_full_alphafold2_standard { includeConfig 'conf/test_full.config' }
test_full_alphafold2_split { includeConfig 'conf/test_full_alphafold_split.config' }
test_full_alphafold2_multimer { includeConfig 'conf/test_full_alphafold_multimer.config' }
test_full_colabfold_local { includeConfig 'conf/test_full_colabfold_local.config' }
test_full_colabfold_webserver { includeConfig 'conf/test_full_colabfold_webserver.config' }
test_full_colabfold_multimer { includeConfig 'conf/test_full_colabfold_webserver_multimer.config' }
test_full_esmfold { includeConfig 'conf/test_full_esmfold.config' }
test_full_esmfold_multimer { includeConfig 'conf/test_full_esmfold_multimer.config' }
test_rosettafold_all_atom { includeConfig 'conf/test_rosettafold_all_atom.config' }
test_helixfold3 { includeConfig 'conf/test_helixfold3.config' }
}
// Load nf-core custom profiles from different Institutions
try {
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/proteinfold custom profiles from different institutions.
try {
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/proteinfold.config" : "/dev/null"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/proteinfold profiles: ${params.custom_config_base}/pipeline/proteinfold.config")
}
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
charliecloud.registry = 'quay.io'
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Set bash options
process.shell = """\
bash
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
"""
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}
manifest {
name = 'nf-core/proteinfold'
author = """Athanasios Baltzis, Jose Espinosa-Carrasco, Harshil Patel""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
contributors = [
// TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
[
name: 'Athanasios Baltzis',
affiliation: 'Centre for Genomic Regulation, Spain',
email: '',
github: 'athbaltzis',
contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: '0000-0002-7495-1218'
],
[
name: ' Jose Espinosa-Carrasco',
affiliation: 'Centre for Genomic Regulation, Spain',
email: '[email protected]',
github: 'joseespinosa',
contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: '0000-0002-1541-042X'
],
[
name: ' Harshil Patel',
affiliation: '',
email: '',
github: '',
contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: ''
],
]
homePage = 'https://github.com/nf-core/proteinfold'
description = """Protein 3D structure prediction pipeline"""
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=24.04.2'
version = '1.2.0dev'
doi = '10.5281/zenodo.7629996'
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
defaultIgnoreParams = ["genomes"]
monochromeLogs = params.monochrome_logs
help {
enabled = true
command = "nextflow run nf-core/proteinfold -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
beforeText = """
-\033[2m----------------------------------------------------\033[0m-
\033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m
\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m
\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m
\033[0;32m`._,._,\'\033[0m
\033[0;35m nf-core/proteinfold ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/proteinfold/blob/master/CITATIONS.md
"""
}
summary {
beforeText = validation.help.beforeText
afterText = validation.help.afterText
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Load modules config for pipeline specific modes
if (params.mode.toLowerCase().split(",").contains("alphafold2")) {
includeConfig 'conf/modules_alphafold2.config'
}
if (params.mode.toLowerCase().split(",").contains("colabfold")) {
includeConfig 'conf/modules_colabfold.config'
}
if (params.mode.toLowerCase().split(",").contains("esmfold")) {
includeConfig 'conf/modules_esmfold.config'
}
if (params.mode.toLowerCase().split(",").contains("rosettafold_all_atom")) {
includeConfig 'conf/modules_rosettafold_all_atom.config'
}
if (params.mode.toLowerCase().split(",").contains("helixfold3")) {
includeConfig 'conf/modules_helixfold3.config'
}
// Load links to DBs and parameters
includeConfig 'conf/dbs.config'