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Merge pull request #356 from b97pla/uppmax_miarka_config

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removed process-specific requirements for sarek, request miarka high-…
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Phil Ewels 2022-03-24 14:33:06 +01:00 committed by GitHub
commit 7d72e8d94b
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3 changed files with 1 additions and 10 deletions
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7
conf/pipeline/sarek/uppmax.config
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@ -30,11 +30,4 @@ if (hostname ==~ "i.*") {
// Miarka-specific config // Miarka-specific config
if (hostname ==~ "m.*") { if (hostname ==~ "m.*") {
params.single_cpu_mem = 7.GB params.single_cpu_mem = 7.GB
process {
withName:MapReads {
cpus = {params.max_cpus}
memory = {params.max_memory}
}
}
} }

3
conf/uppmax.config
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@ -47,7 +47,7 @@ def clusterOptionsCreator = { m ->
return base + " --mem 2TB " return base + " --mem 2TB "
} }
// job requires the largest node // job requires the largest node
return base + " --mem 4TB " return base + " -C mem4TB "
} }
if (m <= 250.GB) { if (m <= 250.GB) {
@ -94,7 +94,6 @@ if (hostname.startsWith("i")) {
// Cluster: Miarka // Cluster: Miarka
if (hostname.startsWith("m")) { if (hostname.startsWith("m")) {
params.max_memory = 357.GB params.max_memory = 357.GB
// but what about the 96-core node?
params.max_cpus = 48 params.max_cpus = 48
params.max_time = 480.h params.max_time = 480.h
params.config_profile_description = 'UPPMAX (Miarka) cluster profile provided by nf-core/configs.' params.config_profile_description = 'UPPMAX (Miarka) cluster profile provided by nf-core/configs.'

1
docs/pipeline/sarek/uppmax.md
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@ -15,4 +15,3 @@ Example: `nextflow run nf-core/sarek -profile uppmax`
Specific configurations for uppmax clusters has been made for sarek. Specific configurations for uppmax clusters has been made for sarek.
- Set paths to reference genomes - Set paths to reference genomes
- Override resource requirements for MapReads on `miarka`