Newer
Older
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
/*
* -------------------------------------------------
* nf-core/hic Nextflow config file
* -------------------------------------------------
* Default config options for all environments.
* Cluster-specific config options should be saved
* in the conf folder and imported under a profile
* name here.
*/
// Global default params, used in configs
params {
// Container slug. Stable releases should specify release tag!
// Developmental code should specify :latest
container = 'nfcore/hic:latest'
// Workflow flags
// TODO nf-core: Specify your pipeline's command line flags
reads = "data/*{1,2}.fastq.gz"
singleEnd = false
outdir = './results'
// Boilerplate options
name = false
multiqc_config = "$baseDir/conf/multiqc_config.yaml"
email = false
plaintext_email = false
help = false
igenomes_base = "./iGenomes"
tracedir = "${params.outdir}/pipeline_info"
clusterOptions = false
awsqueue = false
awsregion = 'eu-west-1'
igenomesIgnore = false
custom_config_version = 'master'
}
// 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' }
}
// Load igenomes.config if required
if(!params.igenomesIgnore){
includeConfig 'conf/igenomes.config'
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = true
file = "${params.tracedir}/nf-core/hic_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/nf-core/hic_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/nf-core/hic_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/nf-core/hic_dag.svg"
}
manifest {
name = 'nf-core/hic'
author = 'Nicolas Servant'
homePage = 'https://github.com/nf-core/hic'
description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
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
}
}
}