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comparison ui/assets/config/executor/slurm.config @ 0:d9c5c5b87fec draft

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planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
author fubar
date Sat, 03 Aug 2024 11:16:53 +0000
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-1:000000000000 0:d9c5c5b87fec
1 // Config for typical SLURM cluster
2 // Adjust the parameters for your cluster - queue name, temp dir, etc.
3 // Use your temp space instead of /data/$USER in the following config
4
5 singularity {
6 enabled = true
7 autoMounts = true
8 cacheDir = "/data/$USER/singularity"
9 envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOB_ID,SINGULARITY_BINDPATH'
10 }
11
12 env {
13 SINGULARITY_CACHEDIR="/data/$USER/singularity"
14 SINGULARITY_TMPDIR="/data/$USER/tmp"
15 }
16
17 process {
18 executor = 'slurm'
19 // Set other parameters specific to your cluser here
20 // maxRetries = 1
21 // queue = 'norm'
22 // queueSize = 200
23 // pollInterval = '2 min'
24 // queueStatInterval = '5 min'
25 // submitRateLimit = '6/1min'
26 // retry.maxAttempts = 1
27
28 // clusterOptions = ' --gres=lscratch:200 '
29
30 // scratch = '/lscratch/$SLURM_JOB_ID'
31 // with the default stageIn and stageOut settings using scratch can
32 // result in humungous work folders
33 // see https://github.com/nextflow-io/nextflow/issues/961 and
34 // https://www.nextflow.io/docs/latest/process.html?highlight=stageinmode
35 //stageInMode = 'symlink'
36 //stageOutMode = 'rsync'
37 }