-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathnextflow.config
More file actions
75 lines (65 loc) · 2.13 KB
/
nextflow.config
File metadata and controls
75 lines (65 loc) · 2.13 KB
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
plugins {
id '[email protected]'
}
validation {
help {
enabled = true
shortParameter = false
fullParameter = 'help'
showHidden = true
afterText = 'If you encounter any issues with fold2go, please report them at https://gitlab.rlp.net/imbforge/fold2go/-/issues'
}
}
// include the pipeline config defaults
includeConfig 'workflows/fold2go/nextflow.config'
// include pipeline profiles
// these should at least configure executor, container engine and 'gpu' process label
profiles {
standard {
includeConfig 'configs/singularity.config'
includeConfig 'configs/imb.config'
}
docker {
includeConfig 'configs/docker.config'
}
singularity {
includeConfig 'configs/singularity.config'
}
}
// generate a timestamp to add to reports
def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm')
report {
enabled = true
overwrite = true
file = "${params.OUT}/report_${timestamp}.html"
}
timeline {
enabled = true
overwrite = true
file = "${params.OUT}/timeline_${timestamp}.html"
}
trace {
enabled = false
overwrite = true
file = "${params.OUT}/trace_${timestamp}.txt"
}
dag {
enabled = false
overwrite = true
file = "${params.OUT}/graph_${timestamp}.mmd"
}
manifest {
name = 'imbforge/fold2go'
homePage = 'https://gitlab.rlp.net/imbforge/fold2go'
description = 'fold2go is a nextflow pipeline for in silico prediction of protein structures and interactions through various machine learning models'
author = 'Patrick Hüther ([email protected])'
mainScript = 'main.nf'
defaultBranch = 'main'
nextflowVersion = '!>=24.04.0'
}
// when a run is terminated via GUI, the jupyter-server is not stopped, which leads to a 500 error
// workaround this by manually stopping the jupyter-server, which will shut the proxy down as well
// FIXME: once https://github.com/jupyterhub/jupyter-server-proxy/pull/395 is merged, this can be handled programmatically
if ( System.getenv('JUPYTERHUB_SERVICE_URL') ) {
workflow.onComplete = { "jupyter-server stop ${new URL(System.getenv('JUPYTERHUB_SERVICE_URL')).getPort()}".execute() }
}