forked from epi2me-labs/wf-artic
-
Notifications
You must be signed in to change notification settings - Fork 0
/
nextflow.config
161 lines (141 loc) · 4.19 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
//
// Notes to End Users.
//
// The workflow should run without editing this configuration file,
// however there may be instances in which you wish to edit this
// file for compute performance or other reasons. Please see:
//
// https://nextflow.io/docs/latest/config.html#configuration
//
// for further help editing this file.
params {
help = false
version = false
out_dir = "output"
artic_threads = 4
squirrel_threads = 4
squirrel_options = false
analyse_unclassified = false
skip_squirrel = false
fastq = null
sample = null
sample_sheet = null
min_reads = 1000
min_len = null
max_len = null
max_softclip_length = null
normalise = 200
override_basecaller_cfg = null
scheme_name = "MPXV"
scheme_version = "yale-mpox/v1.0.0-cladeI"
list_schemes = false
custom_scheme = null
aws_image_prefix = null
aws_queue = null
disable_ping = false
lab_id = null
testkit = null
monochrome_logs = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf'
wf {
example_cmd = [
"--fastq 'wf-artic-demo/fastq'",
"--sample_sheet 'wf-artic-demo/sample_sheet.csv'",
"--scheme_name 'SARS-CoV-2'",
"--scheme_version 'Midnight-ONT/V3'"
]
common_sha = 'sha8b5843d549bb210558cbb676fe537a153ce771d6'
container_sha = 'sha15e9dfa0469ddd0641dfe1a5f07bedb475a8a03d'
}
}
manifest {
name = 'artic-network/artic-mpxv-nf'
author = 'Oxford Nanopore Technologies. artic-network: Sam Wilkinson, Rachel Colquhoun'
homePage = 'https://github.com/artic-network/artic-mpxv-nf'
description = 'Run the ARTIC fieldbioinformatics workflow on multiplexed MPXV ONT data'
mainScript = 'main.nf'
nextflowVersion = '>=23.04.2'
version = 'v1.1.1'
}
epi2melabs {
tags = 'mpox,artic,amplicon,viruses,public health'
icon = 'faVirusCovid'
}
env {
PYTHONNOUSERSITE = 1
JAVA_TOOL_OPTIONS = "-Xlog:disable -Xlog:all=warning:stderr"
}
process {
withLabel:wf_common {
container = "ontresearch/wf-common:${params.wf.common_sha}"
memory = '1G'
}
withLabel:artic {
container = "quay.io/artic/fieldbioinformatics:1.4.1"
memory = { 4.GB * task.attempt }
}
withLabel:squirrel {
container = "community.wave.seqera.io/library/squirrel:1.0.10--dc85d171b951f751"
memory = '2G'
}
shell = ['/bin/bash', '-euo', 'pipefail']
}
profiles {
// the "standard" profile is used implicitely by nextflow
// if no other profile is given on the CLI
standard {
docker {
enabled = true
// this ensures container is run as host user and group, but
// also adds host user to the within-container group
runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
}
}
// using singularity instead of docker
singularity {
singularity {
enabled = true
autoMounts = true
}
}
// keep stub conda profile to prevent unknown profile warning so users get a better error
conda {
conda.enabled = true // for nextflow >=22.08
}
awsbatch {
process {
executor = 'awsbatch'
queue = "${params.aws_queue}"
withLabel:wf_common {
container = "${params.aws_image_prefix}-wf-common:${params.wf.common_sha}"
memory = '1G'
}
withLabel:artic {
container = "${params.aws_image_prefix}-wf-artic:${params.wf.container_sha}"
memory = '2G'
}
shell = ['/bin/bash', '-euo', 'pipefail']
}
}
// local profile for simplified development testing
local {
process.executor = 'local'
}
}
timeline {
enabled = true
overwrite = true
file = "${params.out_dir}/execution/timeline.html"
}
report {
enabled = true
overwrite = true
file = "${params.out_dir}/execution/report.html"
}
trace {
enabled = true
overwrite = true
file = "${params.out_dir}/execution/trace.txt"
}