diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index b563828..e1a347b 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -191,10 +191,18 @@ process { withName:get_software_versions { cache = false - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } + + 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 { @@ -374,13 +382,6 @@ profiles { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } } - - withName:get_software_versions { - cache = false - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } - } - } } @@ -560,13 +561,6 @@ profiles { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' } } - - withName:get_software_versions { - cache = false - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } - } - } }