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Merge pull request #1 from TCLamnidis/TCLamnidis-patch-1
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commit
08edd19d67
1 changed files with 9 additions and 15 deletions
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@ -191,10 +191,18 @@ process {
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withName:get_software_versions {
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cache = false
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName:kraken_merge {
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beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
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}
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withName:multiqc {
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beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1;'
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}
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}
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profiles {
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@ -374,13 +382,6 @@ profiles {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
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}
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withName:get_software_versions {
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cache = false
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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}
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}
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@ -560,13 +561,6 @@ profiles {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
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}
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withName:get_software_versions {
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cache = false
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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}
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}
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