forked from IARCbioinfo/bam2cram-nf
-
Notifications
You must be signed in to change notification settings - Fork 0
/
nextflow.config
69 lines (65 loc) · 1.39 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
manifest {
homePage = 'https://github.com/adigenova/bam2cram'
description = 'bam to cram conversion'
mainScript = 'main.nf'
version = 2.0
}
params{
// we star coding the pipeline
help = null
bams = null
bam_csv = null
fasta= null
fai = null
debug= false
outdir= "results"
}
profiles {
conda {
process.conda = "$baseDir/environment.yml"
conda.createTimeout = "200 min"
}
docker {
docker.enabled = true
process.container = 'adigenova/bam2cram:v1.0'
}
singularity {
singularity.enabled = true
singularity.autoMonts = true
process.container = 'adigenova/bam2cram:v1.0'
pullTimeout = "200 min"
}
kutral{
singularity.enabled = true
singularity.autoMonts = true
process.container = 'adigenova/bam2cram:v1.0'
pullTimeout = "200 min"
singularity.runOptions = ' --bind /mnt/beegfs/labs/ '
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
process.executor = 'slurm'
process.queue = 'uohhm'
}
}
process {
shell = ['/bin/bash','-o','pipefail']
//process requirements for running
withName: bam2cram {
memory = 10.GB
cpus = 1
}
withName: stats_bams{
memory = 10.GB
cpus = 1
}
withName: stats_crams{
memory = 10.GB
cpus = 1
}
withName: check_conversion{
memory = 10.GB
cpus = 1
}
}