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Add genotyping_ug to SGE fixes

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James A. Fellows Yates 2021-08-20 10:11:11 +02:00 committed by GitHub
parent b0e344846d
commit 6701354060
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1 changed files with 13 additions and 1 deletions
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12
conf/pipeline/eager/eva.config
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@ -125,6 +125,10 @@ process {
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
} }
withName: genotyping_ug {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
} }
profiles { profiles {
@ -260,6 +264,10 @@ profiles {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
} }
withName: genotyping_ug {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
}
withName: preseq { withName: preseq {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" } clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(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' }
@ -399,6 +407,10 @@ profiles {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
} }
withName: genotyping_ug {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
}
withName: preseq { withName: preseq {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" } clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(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' }