This repository has been archived by the owner on Jan 27, 2020. It is now read-only.
forked from nf-core/sarek
-
Notifications
You must be signed in to change notification settings - Fork 6
/
aws-batch.config
65 lines (58 loc) · 2.23 KB
/
aws-batch.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
/*
* -------------------------------------------------
* Nextflow config file for Sarek
* -------------------------------------------------
* Imported under the 'aws' Nextflow profile in nextflow.config
* Defines reference genomes, using paths from s3
* To be use with AWS Batch
*/
params {
genome_base = params.genome == 'GRCh37' ? "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37" : params.genome == 'GRCh38' ? "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38" : "s3://sarek-references/small"
publishDirMode = 'copy'
singleCPUMem = 7.GB // To make the uppmax slurm copy paste work.
localReportDir = 'Reports'
}
executor {
name = 'awsbatch'
awscli = '/home/ec2-user/miniconda/bin/aws'
}
/* Rolling files are currently not supported on s3 */
report.file = "${params.localReportDir}/Sarek_report.html"
timeline.file = "${params.localReportDir}/Sarek_timeline.html"
dag.file = "${params.localReportDir}/Sarek_DAG.svg"
trace.file = "${params.localReportDir}/Sarek_trace.txt"
process {
queue = params.awsqueue
errorStrategy = {task.exitStatus == 143 ? 'retry' : 'terminate'}
maxErrors = '-1'
maxRetries = 4
cpus = 2
memory = 8.GB
time = { check_max( 18.h * task.attempt, 'time' ) }
scratch = true
withName:RunBcftoolsStats {
cpus = 1
memory = {params.singleCPUMem * 2} // Memory is doubled so that it won't run two on the same instance
// Use a tiny queue for this one, so storage doesn't run out
queue = params.awsqueue_tiny
}
withName:RunVcftools {
cpus = 1
memory = {params.singleCPUMem * 2} // Memory is doubled so that it won't run two on the same instance
// Use a tiny queue for this one, so storage doesn't run out
queue = params.awsqueue_tiny
}
withName:RunHaplotypecaller {
cpus = 1
// Increase memory quadratically
memory = {params.singleCPUMem * 2} // Memory is doubled so that it won't run two on the same instance
// Use a tiny queue for this one, so storage doesn't run out
queue = params.awsqueue_tiny
}
withName:RunGenotypeGVCFs {
cpus = 1
memory = {params.singleCPUMem * 2} // Memory is doubled so that it won't run two on the same instance
// Use a tiny queue for this one, so storage doesn't run out
queue = params.awsqueue_tiny
}
}