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Merge pull request #368 from TCLamnidis/master

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Update eva.config
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James A. Fellows Yates 2022-05-04 12:32:04 +02:00 committed by GitHub
commit c85342a9c9
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1 changed files with 10 additions and 15 deletions
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conf/pipeline/eager/eva.config
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@ -191,10 +191,19 @@ process {
withName:get_software_versions { withName:get_software_versions {
cache = false cache = false
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)"
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName:kraken_merge {
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
}
withName:multiqc {
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1;'
}
} }
profiles { profiles {
@ -374,13 +383,6 @@ profiles {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
} }
withName:get_software_versions {
cache = false
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
} }
} }
@ -560,13 +562,6 @@ profiles {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
} }
withName:get_software_versions {
cache = false
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
} }
} }