-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathnextflow.config
executable file
·238 lines (226 loc) · 7.77 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
manifest {
description = 'Synteny analysis'
author = 'Chris Wyatt and Simon Murray'
}
// Defaults parameters, expecting to be overwritten
params {
// Path to results directory
outdir = "results"
// Path to input CSV
input = null
hex = "s3://synteny-test-data/data/unique_hex"
go = null
tree = null
ribbon = null
score = null
chromopaint = false
lifted = true
cutoff = "10,20"
gffread_coding = null
jcvi_ortholog_arguments = "--no_strip_names"
jcvi_screen_arguments = "--minspan 20"
// Remove work directories upon pipeline completion
clean = false
// Architecture of platform pipeline is running on
architecture = "amd"
// include basic config
custom_config = null
// Max resource options
max_memory = '128.GB'
max_cpus = 16
max_time = '48.h'
// Display help message with nf-validation
help = null
// nf-core module parameters
publish_dir_mode = 'copy'
params.seqkit_basename = null
params.seqkit_fq_encoding = null
params.seqkit_gap_letters = null
}
plugins {
id '[email protected]'
id '[email protected]'
id '[email protected]'
}
def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
co2footprint {
traceFile = "${params.outdir}/pipeline_info/co2_emissions/co2footprint_trace_${timestamp}.txt"
reportFile = "${params.outdir}/pipeline_info/co2_emissions/co2footprint_report_${timestamp}.html"
summaryFile = "${params.outdir}/pipeline_info/co2_emissions/co2footprint_summary_${timestamp}.html"
ci = 300
pue = 1.4
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load custom config if provided
if (params.custom_config != null) {
try {
includeConfig "${params.custom_config}"
} catch (Exception e) {
System.err.println("WARNING: Could not load config: ${params.custom_config}")
}
}
// Select a combination of useful profiles i.e. nextflow run -profile local,docker
profiles {
aws_batch {
includeConfig 'conf/aws_batch.config'
}
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_full { includeConfig 'conf/test_full.config' }
test_mammal { includeConfig 'conf/test_mammal.config' }
test_halictids { includeConfig 'conf/test_halictids.config' }
}
// Load nf-core modules config
includeConfig 'conf/modules.config'
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
// Capturing Nextflow log files into a rsults/pipeline_info directory
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${timestamp}.html"
}
// Ensures work directories and removed when pipeline completes
if (params.clean == true) {
cleanup = true
}
// 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
}
}
}