This repository has been archived by the owner on Dec 17, 2021. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathnextflow.config
99 lines (90 loc) · 2.77 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
params {
container = 'quay.io/eqtlcatalogue/susie-finemapping:v20.08.1'
outdir = './results'
custom_config_version = 'master'
tracedir = "${params.outdir}/pipeline_info"
}
profiles {
tartu_hpc { includeConfig 'conf/tartu_hpc.config'}
finemapping {
includeConfig 'conf/tartu_hpc.config'
includeConfig 'conf/finemapping.config'
}
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
includeConfig "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/nfcore_custom.config"
profiles {
awsbatch { includeConfig 'conf/awsbatch.config' }
conda { process.conda = "$baseDir/environment.yml" }
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
process.container = params.container
}
singularity {
singularity.enabled = true
process.container = {"shub://${params.container.replace('nfcore', 'nf-core')}"}
}
test { includeConfig 'conf/test.config' }
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = true
file = "${params.tracedir}/nf-core/qtlmap_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/nf-core/qtlmap_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/nf-core/qtlmap_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/nf-core/qtlmap_dag.svg"
}
manifest {
name = 'nf-core/qtlmap'
author = 'Nurlan Kerimov'
homePage = 'https://github.com/nf-core/qtlmap'
description = 'This pipeline mapping "Quantitive Trait Loci"-s'
mainScript = 'main.nf'
nextflowVersion = '>=0.32.0'
version = '1.0dev'
}
// 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
}
}
}