-
Notifications
You must be signed in to change notification settings - Fork 117
/
nextflow.config
401 lines (375 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
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/ampliseq Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
input_fasta = null
input_folder = null
multiregion = null
extension = "/*_R{1,2}_001.fastq.gz"
pacbio = false
iontorrent = false
FW_primer = null
RV_primer = null
classifier = null
metadata = null
// Other options
save_intermediates = false
trunc_qmin = 25
trunc_rmin = 0.75
trunclenf = null
trunclenr = null
max_ee = 2
max_len = null
ignore_failed_filtering = false
min_len = 50
metadata_category = null
metadata_category_barplot = null
double_primer = false
retain_untrimmed = false
cutadapt_min_overlap = 3
cutadapt_max_error_rate = 0.1
exclude_taxa = "mitochondria,chloroplast"
min_frequency = 1
min_samples = 1
multiple_sequencing_runs = false
single_end = false
sample_inference = "independent"
illumina_novaseq = false
illumina_pe_its = false
concatenate_reads = false
cut_its = "none"
its_partial = 0
picrust = false
sbdiexport = false
addsh = false
tax_agglom_min = 2
tax_agglom_max = 6
min_read_counts = 1
ignore_failed_trimming = false
ignore_empty_input_files = false
qiime_adonis_formula = null
seed = 100
filter_ssu = null
min_len_asv = null
max_len_asv = null
filter_codons = null
orf_start = 1
orf_end = null
stop_codons = "TAA,TAG"
pplace_tree = null
pplace_aln = null
pplace_model = null
pplace_alnmethod = 'hmmer'
pplace_taxonomy = null
pplace_name = null
diversity_rarefaction_depth= 500
ancom_sample_min_count = 1
vsearch_cluster = null
vsearch_cluster_id = 0.97
ancom = false
ancombc = false
ancombc_effect_size = 1
ancombc_significance = 0.05
ancombc_formula = null
ancombc_formula_reflvl = null
// Report options
report_template = "${projectDir}/assets/report_template.Rmd"
report_css = "${projectDir}/assets/nf-core_style.css"
report_logo = "${projectDir}/assets/nf-core-ampliseq_logo_light_long.png"
report_title = "Summary of analysis results"
report_abstract = null
// Skipping options
skip_cutadapt = false
skip_dada_quality = false
skip_barrnap = false
skip_qiime = false
skip_qiime_downstream = false
skip_fastqc = false
skip_alpha_rarefaction = false
skip_abundance_tables = false
skip_barplot = false
skip_taxonomy = false
skip_dada_taxonomy = false
skip_dada_addspecies = false
skip_alpha_rarefaction = false
skip_diversity_indices = false
skip_multiqc = false
skip_report = false
// Database options
dada_ref_taxonomy = "silva=138"
dada_assign_taxlevels = null
dada_ref_tax_custom = null
dada_ref_tax_custom_sp = null
cut_dada_ref_taxonomy = false
dada_addspecies_allowmultiple = false
dada_taxonomy_rc = false
sintax_ref_taxonomy = null
qiime_ref_taxonomy = null
qiime_ref_tax_custom = null
kraken2_ref_taxonomy = null
kraken2_assign_taxlevels = null
kraken2_ref_tax_custom = null
kraken2_confidence = 0.0
sidle_ref_taxonomy = null
sidle_ref_tax_custom = null
sidle_ref_tree_custom = null
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'dada_ref_databases,qiime_ref_databases,sintax_ref_databases,kraken2_ref_databases,sidle_ref_databases,genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/ampliseq custom profiles from different institutions.
try {
includeConfig "${params.custom_config_base}/pipeline/ampliseq.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/ampliseq profiles: ${params.custom_config_base}/pipeline/ampliseq.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', 'defaults']
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_single { includeConfig 'conf/test_single.config' }
test_multi { includeConfig 'conf/test_multi.config' }
test_doubleprimers { includeConfig 'conf/test_doubleprimers.config' }
test_pacbio_its { includeConfig 'conf/test_pacbio_its.config' }
test_iontorrent { includeConfig 'conf/test_iontorrent.config' }
test_fasta { includeConfig 'conf/test_fasta.config' }
test_failed { includeConfig 'conf/test_failed.config' }
test_full { includeConfig 'conf/test_full.config' }
test_reftaxcustom { includeConfig 'conf/test_reftaxcustom.config' }
test_qiimecustom { includeConfig 'conf/test_qiimecustom.config' }
test_novaseq { includeConfig 'conf/test_novaseq.config' }
test_pplace { includeConfig 'conf/test_pplace.config' }
test_sintax { includeConfig 'conf/test_sintax.config' }
test_its_dada_taxonomy { includeConfig 'conf/test_its_dada_taxonomy.config' }
test_multiregion { includeConfig 'conf/test_multiregion.config' }
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / 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'
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
// 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"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
// 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-core/ampliseq'
author = """Daniel Straub, Alexander Peltzer"""
homePage = 'https://github.com/nf-core/ampliseq'
description = """Amplicon sequencing analysis workflow using DADA2 and QIIME2"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '2.11.0'
doi = '10.5281/zenodo.1493841,10.3389/fmicb.2020.550420'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Load ref_databases.config for reference taxonomy
includeConfig 'conf/ref_databases.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}