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Merge pull request #314 from jfy133/master

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Update eager@eva to add java buffer for bbduk
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James A. Fellows Yates 2022-01-14 07:40:56 +01:00 committed by GitHub
commit 4546e0f389
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1 changed files with 12 additions and 0 deletions
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conf/pipeline/eager/eva.config
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@ -100,6 +100,10 @@ process {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
memory = { check_max( 4.GB * task.attempt, 'memory' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) }
} }
withName: metagenomic_complexity_filter {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: malt { withName: malt {
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
@ -258,6 +262,10 @@ profiles {
memory = { check_max( 4.GB * task.attempt, 'memory' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) }
} }
withName: metagenomic_complexity_filter {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: malt { withName: malt {
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
cpus = { check_max( 32, 'cpus' ) } cpus = { check_max( 32, 'cpus' ) }
@ -425,6 +433,10 @@ profiles {
time = 1440.h time = 1440.h
} }
withName: metagenomic_complexity_filter {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: malt { withName: malt {
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
cpus = { check_max( 32, 'cpus' ) } cpus = { check_max( 32, 'cpus' ) }