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Merge pull request #248 from jfy133/eva

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Fix MakeSeqDict eager @ eva
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James A. Fellows Yates 2021-06-07 13:26:05 +02:00 committed by GitHub
commit 756f067213
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1 changed files with 6 additions and 2 deletions
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conf/pipeline/eager/eva.config
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@ -61,7 +61,7 @@ process {
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
withName: makeSeqDict { withName: makeSeqDict {
clusterOptions = { "-S /bin/bash -v JAVA_OPTS='-XX:ParallelGCThreads=1' -l h_vmem=${(task.memory.toGiga() + 3)}G,virtual_free=${(task.memory.toGiga() + 3)}G" } clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
} }
withName: fastqc { withName: fastqc {
@ -79,6 +79,10 @@ process {
withName: markduplicates { withName: markduplicates {
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: library_merge {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
}
withName: malt { withName: malt {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
@ -212,4 +216,4 @@ profiles {
bwaalnl = 16500 bwaalnl = 16500
} }
} }
} }