-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathnextflow.config
executable file
·268 lines (239 loc) · 8.67 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
/*
========================================================================================
ARETE Nextflow config file
========================================================================================
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input_sample_table = null
// Database cache
db_cache = null
// PopPunk
skip_poppunk = false
poppunk_model = null
run_poppunk_qc = false
// Subsampling parameters
enable_subsetting = false
core_similarity = 99.9
accessory_similarity = 99
// Phylogenomics parameters
skip_phylo = false
use_ppanggolin = false
use_full_alignment = false
use_fasttree = true
// Annotation parameters
use_prokka = false
bakta_db = null
annotation_tools = 'mobsuite,rgi,cazy,vfdb,iceberg,bacmet,islandpath,phispy,report'
feature_profile_columns = 'mobsuite,rgi,cazy,vfdb,iceberg,bacmet'
feature_dispersion_columns = null
upset_plot_columns = null
min_pident = 60
min_qcover = 0.6
skip_profile_creation = false
// References
reference_genome = null
// Kraken2
skip_kraken = false
// Gene Order
run_gene_order = false
input_file_path = "$projectDir/test/gene-order/rgi_input.txt"
gene_order_percent_cutoff = 0.25
gene_order_label_cols = null
num_neighbors = 10
// Optional clustering module hyperparameter options
inflation = 2
epsilon = 0.5
minpts = 5
plot_clustering = false
// QC options
run_checkm = false
apply_filtering = false
min_n50 = 10000
min_contigs_1000_bp = 1
min_contig_length = 1
// Recombination
run_recombination = false
run_verticall = true
run_gubbins = false
// Dynamics
run_evolccm = false
run_rspr = false
min_rspr_distance = 10
min_branch_length = 0
max_support_threshold = 0.7
max_approx_rspr = -1
min_heatmap_approx_rspr = 0
max_heatmap_approx_rspr = -1
min_heatmap_exact_rspr = 0
max_heatmap_exact_rspr = -1
// rSPR/evolCCM entries
core_gene_tree = null
concatenated_annotation = null
feature_profile = null
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = "$projectDir/assets/arete-logo-transparent.png"
max_multiqc_email_size = '25.MB'
// Boilerplate options
outdir = './results'
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,modules'
enable_conda = false
singularity_pull_docker_container = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = [:]
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '125.GB'
max_cpus = 72
max_time = '168.h'
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.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")
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
light { includeConfig 'conf/light.config' }
small { includeConfig 'conf/base.config' }
medium { includeConfig 'conf/medium.config' }
large { includeConfig 'conf/large.config' }
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
}
manifest {
name = 'beiko-lab/ARETE'
author = 'Finlay Maguire'
homePage = 'https://github.com/beiko-lab/arete'
description = 'AMR/VF LGT-focused bacterial genomics workflow'
mainScript = 'main.nf'
nextflowVersion = '!>=22.10.6'
version = '1.0.1'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}