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Merge pull request #180 from MaxUlysse/rackham

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Rackham
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Johannes Alneberg 2020-09-29 10:31:04 +02:00 committed by GitHub
commit 59cd8d69ed
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2 changed files with 12 additions and 5 deletions
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15
conf/pipeline/sarek/uppmax.config
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@ -4,18 +4,25 @@ params {
config_profile_contact = 'Maxime Garcia (@MaxUlysse)' config_profile_contact = 'Maxime Garcia (@MaxUlysse)'
config_profile_description = 'nf-core/sarek uppmax profile provided by nf-core/configs' config_profile_description = 'nf-core/sarek uppmax profile provided by nf-core/configs'
singleCPUmem = 7000.MB single_cpu_mem = 7000.MB
// Just useful until iGenomes is updated on UPPMAX // Just useful until iGenomes is updated on UPPMAX
igenomeIgnore = true igenomes_ignore = true
genomes_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : '/sw/data/uppnex/ToolBox/hg38bundle' genomes_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : '/sw/data/uppnex/ToolBox/hg38bundle'
} }
def hostname = "hostname".execute().text.trim() def hostname = "hostname".execute().text.trim()
if (hostname ==~ "r.*") { if (hostname ==~ "r.*") {
params.singleCPUmem = 6400.MB params.single_cpu_mem = 6400.MB
process {
withName:BamQC {
cpus = {params.max_cpus}
memory = {params.max_memory}
}
}
} }
if (hostname ==~ "i.*") { if (hostname ==~ "i.*") {
params.singleCPUmem = 15.GB params.single_cpu_mem = 15.GB
} }

2
conf/uppmax.config
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@ -15,7 +15,7 @@ process {
} }
params { params {
saveReference = true save_reference = true
max_memory = 125.GB max_memory = 125.GB
max_cpus = 16 max_cpus = 16