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Move beforeScript exports to env scope

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This commit is contained in:
James Fellows Yates 2022-06-15 15:21:20 +02:00
parent 9ef52af084
commit 58dd9d49c7
1 changed files with 6 additions and 18 deletions
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24
conf/pipeline/eager/eva.config
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@ -6,11 +6,15 @@ params {
config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs' config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs'
} }
env {
JAVA_TOOL_OPTIONS = "-XX:ParallelGCThreads=1"
OPENBLAS_NUM_THREADS = 1
OMP_NUM_THREADS = 1
}
// Specific nf-core/eager process configuration // Specific nf-core/eager process configuration
process { process {
beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
maxRetries = 2 maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
@ -192,22 +196,10 @@ process {
withName:get_software_versions { withName:get_software_versions {
cache = false cache = false
clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" } clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 4)}M" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 4)}M" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName:eigenstrat_snp_coverage {
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
}
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 { profiles {
@ -226,8 +218,6 @@ profiles {
process { process {
beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
maxRetries = 2 maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
@ -404,8 +394,6 @@ profiles {
process { process {
beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
maxRetries = 2 maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion