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Merge pull request #251 from phue/cbe_singularity_workaround

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cbe: send SIGUSR2 upon job termination
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Falko Hofmann 2021-10-04 13:24:53 +02:00 committed by GitHub
commit 0950eb3518
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1 changed files with 4 additions and 2 deletions
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conf/cbe.config
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@ -8,8 +8,10 @@ params {
process { process {
executor = 'slurm' executor = 'slurm'
queue = { task.memory <= 170.GB ? 'c' : 'm' } queue = { task.memory <= 170.GB ? 'c' : 'm' }
clusterOptions = { task.time <= 1.h ? '--qos rapid' : task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' }
module = 'anaconda3/2019.10' module = 'anaconda3/2019.10'
// --signal option will be handled by nextflow after 21.10.0 release (see https://github.com/nextflow-io/nextflow/issues/2163)
clusterOptions = { '--signal B:USR2 ' << ( (queue == 'c' & task.time <= 1.h) ? '--qos rapid' : ( task.time <= 8.h ? '--qos short': ( task.time <= 48.h ? '--qos medium' : '--qos long' ) ) ) }
} }
singularity { singularity {
@ -20,6 +22,6 @@ singularity {
params { params {
params.max_time = 14.d params.max_time = 14.d
params.max_cpus = 36 params.max_cpus = 36
params.max_memory = 4.TB params.max_memory = 1800.GB
igenomes_base = '/resources/references/igenomes' igenomes_base = '/resources/references/igenomes'
} }