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Verified Commit 3856bdcf authored by Laurent Modolo's avatar Laurent Modolo
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update config

parent cbe4c374
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......@@ -4,6 +4,7 @@
process FASTKMERS {
tag "$meta.id"
label 'process_single'
publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
container "lbmc/fastkmers:025efdf"
......
psmn {
charliecloud.enabled = true
charliecloud.cacheDir = "/Xnfs/abc/charliecloud"
charliecloud.readOnlyInputs = true
charliecloud.runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
nextflowVersion = '>=20'
process{
errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
maxRetries = 3
executor = "slurm"
queue = "Lake"
withLabel: process_single {
cpus = 1
memory = "128GB"
time = "24h"
}
withLabel: big_mem_multi_cpus {
cpus = 32
memory = "192GB"
time = "24h"
}
withLabel: small_mem_mono_cpus {
cpus = 1
memory = "16GB"
time = "24h"
}
withLabel: small_mem_multi_cpus {
cpus = 32
memory = "16GB"
time = "24h"
}
}
manifest {
homePage = 'https://gitbio.ens-lyon.fr/LBMC/Delattre/kmer-diff'
description = 'pipeline to quantify kmers'
mainScript = 'main.nf'
version = '0.0.1'
}
report {
enabled = true
file = "$baseDir/../results/report.html"
}
params {
max_memory = 512.GB
max_cpus = 32
max_time = 24.h
profiles {
psmn {
charliecloud.enabled = true
charliecloud.cacheDir = "/Xnfs/abc/charliecloud"
charliecloud.readOnlyInputs = true
charliecloud.runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
process{
errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
maxRetries = 3
executor = "slurm"
queue = "Lake"
withLabel: process_single {
cpus = 1
memory = "128GB"
time = "24h"
}
withLabel: big_mem_multi_cpus {
cpus = 32
memory = "192GB"
time = "24h"
}
withLabel: small_mem_mono_cpus {
cpus = 1
memory = "16GB"
time = "24h"
}
withLabel: small_mem_multi_cpus {
cpus = 32
memory = "16GB"
time = "24h"
}
}
}
}
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