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Move beforeScript exports to env scope
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1 changed files with 6 additions and 18 deletions
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@ -6,11 +6,15 @@ params {
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config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs'
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}
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env {
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JAVA_TOOL_OPTIONS = "-XX:ParallelGCThreads=1"
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OPENBLAS_NUM_THREADS = 1
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OMP_NUM_THREADS = 1
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}
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// Specific nf-core/eager process configuration
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process {
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beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
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maxRetries = 2
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// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
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@ -192,22 +196,10 @@ 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=!(bionode06)" }
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beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"; 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() * 4)}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:eigenstrat_snp_coverage {
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beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
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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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@ -226,8 +218,6 @@ profiles {
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process {
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beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
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maxRetries = 2
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// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
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@ -404,8 +394,6 @@ profiles {
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process {
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beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
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maxRetries = 2
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// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
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