generated from IARCbioinfo/template-nf
-
Notifications
You must be signed in to change notification settings - Fork 0
/
nextflow.config
executable file
·50 lines (43 loc) · 1.05 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
manifest {
homePage = 'https://github.com/iarcbioinfo/metagenomics-nf'
description = 'metagenomics for empty nf pipeline'
mainScript = 'script.nf'
}
profiles {
conda { process.conda = "$baseDir/environment.yml" }
docker {
docker.enabled = true
process.container = 'iarcbioinfo/metagenomics-nf'
}
singularity {
singularity.enabled = true
process.container = null
}
}
process {
shell = ['/bin/bash','-euo','pipefail']
//virusbreakend container for viral integration prediction
withName:"virusbreakend"{
container = "gridss/gridss:latest"
}
}
params {
output_folder = "."
}
timeline {
enabled = true
overwrite = true
file = "${params.output_folder}/nf-pipeline_info/metagenomics_timeline.html"
}
report {
enabled = true
file = "${params.output_folder}/nf-pipeline_info/metagenomics_report.html"
}
trace {
enabled = true
file = "${params.output_folder}/nf-pipeline_info/metagenomics_trace.txt"
}
dag {
enabled = true
file = "${params.output_folder}/nf-pipeline_info/metagenomics_dag.html"
}