-
Notifications
You must be signed in to change notification settings - Fork 18
/
Copy pathnextflow.config
414 lines (386 loc) · 15 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
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/pangenome Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
n_haplotypes = null
// Wfmash options
wfmash_map_pct_id = 90.0
wfmash_segment_length = 5000
wfmash_block_length = null
wfmash_mash_kmer = 19
wfmash_mash_kmer_thres = 0.001
wfmash_sparse_map = 1.0
wfmash_merge_segments = false
wfmash_no_splits = false
wfmash_exclude_delim = null
wfmash_chunks = 1
wfmash_only = false
wfmash_temp_dir = null
wfmash_hg_filter_ani_diff = 30
wfmash_n_mappings = null
// Seqwish options
seqwish_paf = null
seqwish_min_match_length = 23
seqwish_transclose_batch = 10000000
seqwish_sparse_factor = 0.0
seqwish_temp_dir = null
// Smoothxg options
skip_smoothxg = false
smoothxg_max_path_jump = 0
smoothxg_max_edge_jump = 0
smoothxg_poa_length = "700,900,1100"
smoothxg_block_id_min = null
smoothxg_block_ratio_min = 0
smoothxg_pad_max_depth = 100
smoothxg_poa_padding = 0.001
// poa param suggestions from minimap2
// - asm5, --poa-params 1,19,39,3,81,1, ~0.1 divergence
// - asm10, --poa-params 1,9,16,2,41,1, ~1 divergence
// - asm20, --poa-params 1,4,6,2,26,1, ~5% divergence
smoothxg_poa_params = "1,19,39,3,81,1"
smoothxg_write_maf = false
smoothxg_consensus_prefix = "Consensus_"
smoothxg_temp_dir = null
smoothxg_keep_intermediate_files = false
smoothxg_run_abpoa = false
smoothxg_run_global_poa = false
smoothxg_poa_cpus = 0
// Vg deconstruct options
vcf_spec = null
// Community options
communities = 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
validate_params = true
show_hidden_params = false
schema_ignore_params = 'igenomes_base'
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 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
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
process {
resourceLimits = [
memory: 8.GB,
cpus : 4,
time : 1.h
]
}
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf-core/pangenome custom profiles from different institutions.
// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/pangenome.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 = '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/pangenome'
contributors = [
[
name: 'Philipp Ehmele',
affiliation: """Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany""",
email: '',
github: '@imipenem',
contribution: ['contributor'],
orcid: ''
],
[
name: 'Gisela Gabernet',
affiliation: """Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany""",
email: '',
github: '@ggabernet',
contribution: ['contributor'],
orcid: ''
],
[
name: 'Erik Garrison',
affiliation: """University of Tennessee Health Science Center, Memphis, Tennessee, TN, USA""",
email: '',
github: '@ekg',
contribution: ['contributor'],
orcid: ''
],
[
name: 'Andrea Guarracino',
affiliation: """University of Tennessee Health Science Center, Memphis, Tennessee, TN, USA""",
email: '',
github: '@AndreaGuarracino',
contribution: ['contributor'],
orcid: ''
],
[
name: 'Friederike Hanssen',
affiliation: """Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany""",
email: '',
github: '@FriederikeHanssen',
contribution: ['contributor'],
orcid: ''
],
[
name: 'Peter Heringer',
affiliation: """Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany""",
email: '',
github: '@heringerp',
contribution: ['contributor'],
orcid: ''
],
[
name: 'Michael L Heuer',
affiliation: """Mammoth Biosciences, Inc., San Francisco, CA, USA""",
email: '',
github: '@heuermh',
contribution: ['author', 'maintainer'],
orcid: 'https://orcid.org/0000-0002-9052-6000'
],
[
name: 'Lukas Heumos',
affiliation: """Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany""",
email: '',
github: '@zethson',
contribution: ['contributor'],
orcid: ''
],
[
name: 'Simon Heumos',
affiliation: """Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany""",
email: '',
github: '@subwaystation',
contribution: ['author', 'maintainer'],
orcid: 'https://orcid.org/0000-0003-3326-817X'
],
[
name: 'Susanne Jodoin',
affiliation: """Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany""",
email: '',
github: '@SusiJo',
contribution: ['contributor'],
orcid: ''
],
[
name: 'Júlia Mir Pedrol',
affiliation: """Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany""",
email: '',
github: '@mirpedrol',
contribution: ['contributor'],
orcid: ''
],
]
homePage = 'https://github.com/nf-core/pangenome'
description = """The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs"""
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=24.04.2'
version = '1.2.0dev'
doi = 'https://doi.org/10.5281/zenodo.8202636'
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
defaultIgnoreParams = ["genomes"]
lenientMode = true
monochromeLogs = params.monochrome_logs
help {
enabled = true
command = "nextflow run nf-core/pangenome -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/pangenome ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${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/pangenome/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'