-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathnextflow.config
535 lines (472 loc) · 19.5 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
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
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf/pediatric Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
//** Segmentation Options **//
// FastSurfer options
use_fastsurfer = true
fs_license = null
acq3T = true
fs_output_dir = null
// Atlas options
utils_folder = "${projectDir}/assets/FS_BN_GL_SF_utils/"
// MCRIBS options
mcribs_surf = false
mcribs_jointhresh = null
mcribs_fastcollision = false
mcribs_nopialoutside = false
mcribs_cortical = false
mcribs_aparcaseg = false
mcribs_stats = false
mcribs_seed = 1234
//** T1 Preprocessing options **//
// Denoising
t1_denoise_number_of_coils = 1
// N4
t1_bias_bspline_knot_per_voxel = 1
t1_bias_shrink_factor = 1
// Resample
t1_resample_voxel_size = 1
t1_resample_interp = "lin"
// Brain extraction
// Synthstrip
t1_run_synthstrip = false
t1_synthstrip_border = 1
t1_synthstrip_nocsf = false
t1_synthstrip_weights = null
// AntsBet
t1_bet_template = "${projectDir}/assets/templates/t1_template.nii.gz"
t1_bet_template_probability_map = "${projectDir}/assets/templates/t1_brain_probability_map.nii.gz"
//** T2 Preprocessing options **//
// Denoising
t2_denoise_number_of_coils = 1
// N4
t2_bias_bspline_knot_per_voxel = 1
t2_bias_shrink_factor = 1
// Resample
t2_resample_voxel_size = 1
t2_resample_interp = "lin"
// Brain extraction
// Synthstrip
t2_run_synthstrip = false
t2_synthstrip_border = 1
t2_synthstrip_nocsf = false
t2_synthstrip_weights = null
//** Coregistration options **//
// Coregistration
coreg_dimensionality = 3
coreg_transform = "a"
coreg_quick = false
//** DWI Preprocessing options **//
skip_dwi_preprocessing = false
// Denoising
dwi_denoise_patch_size = 7
// Topup
dwi_susceptibility_config_file = "b02b0.cnf"
dwi_susceptibility_output_prefix = "topup_results"
dwi_susceptibility_readout = 0.040
dwi_susceptibility_b0_threshold = 20
dwi_susceptibility_encoding_dir = "y"
// Eddy
dwi_motion_and_eddy_command = "eddy_cpu"
dwi_motion_and_eddy_bet_f_threshold = 0.16
dwi_motion_and_eddy_restore_slices = true
// Powderaverage
dwi_pwdavg_shells = null
dwi_pwdavg_shell_thr = 50
dwi_pwdavg_b0_thr = 20
// Synthstrip
dwi_run_synthstrip = false
dwi_synthstrip_border = 1
dwi_synthstrip_nocsf = false
dwi_synthstrip_weights = null
// FSL bet
dwi_bet_f_threshold = 0.16
dwi_bet_b0_threshold = 20
// N4
dwi_bias_bspline_knot_per_voxel = 0.25
dwi_bias_shrink_factor = 4
// Normalize
dwi_normalize_fa_mask_threshold = 0.4
dwi_normalize_shell_tolerance = 50
// Resample DWI
dwi_resample_voxel_size = 1
dwi_resample_interp = "lin"
// Extract B0
dwi_extract_b0_threshold = 20
// Resample mask
dwi_resample_mask_voxel_size = 1
dwi_resample_mask_interp = "nn"
//** Reconstruction options **//
// DTI Metrics
dti_shell_tolerance = 50
dti_max_shell_value = 1500
dti_b0_threshold = 20
dti_shells = null
// FRF
frf_fa = 0.7
frf_min_fa = 0.5
frf_nvox_min = 300
frf_roi_radius = 20
frf_dwi_shell_tolerance = 50
frf_max_dti_shell_value = 1500
frf_min_fodf_shell_value = 100
frf_b0_threshold = 20
frf_set_method = "ssst"
frf_set_frf = true
frf_manual_frf = "15,4,4"
frf_mean_frf = false
// FODF Metrics
fodf_shell_tolerance = 50
fodf_min_fodf_shell_value = 100
fodf_shells = null
fodf_b0_threshold = 20
fodf_sh_order = 8
fodf_sh_basis = "descoteaux07"
fodf_set_method = "ssst"
fodf_relative_threshold = 0.1
fodf_a_factor = 2.0
fodf_max_fa_threshold = 0.1
fodf_min_md_threshold = 0.003
// ** Registration options ** //
// Apply registration
reg_dimensionality = 3
reg_interpolation = "NearestNeighbor"
reg_output_dtype = "int"
// ** Tracking options ** //
// PFT Tracking
run_pft_tracking = true
pft_fa_threshold = 0.2
pft_seeding_mask_type = "wm"
pft_random_seed = 1234
pft_compress = true
pft_compress_value = 0.2
pft_algo = "prob"
pft_nbr_seeds = 10
pft_seeding_type = "npv"
pft_step = 0.5
pft_theta = 20
pft_sfthres = 0.1
pft_sfthres_init = 0.5
pft_min_len = 20
pft_max_len = 200
pft_particles = 15
pft_back = 2
pft_front = 1
pft_sh_basis = "descoteaux07"
// Local Tracking
run_local_tracking = true
local_fa_tracking_mask_threshold = 0.4
local_fa_seeding_mask_threshold = 0.4
local_seeding_mask_type = "wm"
local_tracking_mask_type = "wm"
local_random_seed = 1234
local_compress = true
local_compress_value = 0.2
local_algo = "prob"
local_nbr_seeds = 10
local_seeding_type = "npv"
local_step = 0.5
local_theta = 20
local_sfthres = 0.1
local_min_len = 20
local_max_len = 200
local_sh_basis = "descoteaux07"
// ** Connectomics Options ** //
// Transform labels options
labels_transform_dimensionality = 3
labels_interpolation = "NearestNeighbor"
labels_output_dtype = "int"
labels_output_suffix = "_labels"
// COMMIT options
run_commit2 = true
commit2_lambda = 0.001
commit_para_diff = null
commit_iso_diff = null
commit_perp_diff = null
commit_ball_stick = false
commit_nbr_dir = 500
commit_shell_tolerance = 20
// Decompose Options
decompose_no_pruning = false
decompose_no_remove_loops = false
decompose_no_remove_outliers = false
decompose_no_remove_curv = false
decompose_min_len = 20
decompose_max_len = 200
decompose_outlier_threshold = 0.6
decompose_max_angle = 330.0
decompose_max_curv = 10.0
// AFD_Fixel Options
afd_fixel_sh_basis = "descoteaux07"
afd_fixel_length_weighting = false
// MultiQC options
multiqc_config = null
multiqc_title_subject = "nf-pediatric MultiQC Subject Report"
multiqc_title_global = "nf-pediatric MultiQC Global Report"
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 = null
// 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
// Profiles options
infant = false
tracking = false
connectomics = false
segmentation = false
// Lean output mode.
lean_output = true
// 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
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
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
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
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
no_symlink {
params.publish_dir_mode = 'copy'
}
slurm {
process {
maxRetries = 1
cache = "lenient"
afterScript = "sleep 60"
}
executor {
name = 'slurm'
queueSize = 1000
queueGlobalStatus = false
queueStatInterval = '3 min'
submitRateLimit = '10/1sec'
exitReadTimeout = '30 min'
pollInterval = '30 sec'
jobName = {
task.name
.replace("[", "(")
.replace("]", ")")
.replace(" ", "_")
}
}
}
infant {
params.infant = true
params.dwi_run_synthstrip = true
params.t1_run_synthstrip = true
params.t2_run_synthstrip = true
params.dwi_normalize_fa_mask_threshold = 0.10
params.frf_manual_frf = "12,5,5"
params.run_pft_tracking = false
params.local_min_len = 15
params.local_fa_seeding_mask_threshold = 0.10
params.commit_para_diff = "1.2E-3"
params.commit_iso_diff = "2.0E-3"
params.decompose_min_len = 10
params.decompose_outlier_threshold = 0.4
}
tracking {
params.tracking = true
}
connectomics {
params.connectomics = true
}
segmentation {
params.segmentation = true
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf/pediatric custom profiles from different institutions.
// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/pediatric.config" : "/dev/null"
// 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 = 'docker.io'
docker.registry = 'docker.io'
podman.registry = 'quay.io'
singularity.registry = 'docker.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
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'nf/pediatric'
author = """Anthony Gagnon"""
homePage = 'https://github.com/nf/pediatric'
description = """nf-pediatric is a neuroimaging pipeline to process pediatric MRI data (including fMRI, dMRI, and sMRI) ranging from 0-18 years old."""
mainScript = 'main.nf'
nextflowVersion = '!>=24.10.0'
version = '1.0dev'
doi = ''
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
defaultIgnoreParams = ["genomes"]
help {
enabled = true
command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
}
}