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Merge pull request #382 from jfy133/eva-java-correction

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EAGER @ EVA Further Java workarounds
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James A. Fellows Yates 2022-07-04 13:42:13 +02:00 committed by GitHub
commit 08435ca300
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1 changed files with 15 additions and 23 deletions
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38
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_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_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
@ -69,17 +73,17 @@ process {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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: fastqc_after_clipping { withName: fastqc_after_clipping {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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: adapter_removal { withName: adapter_removal {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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: bwa { withName: bwa {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
} }
@ -188,26 +192,18 @@ process {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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: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_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 8)}M" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 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 { withName:multiqc {
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1;' clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga() * 2}G" }
} }
} }
profiles { profiles {
@ -226,8 +222,6 @@ profiles {
process { process {
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
maxRetries = 2 maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
@ -279,7 +273,7 @@ profiles {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: fastqc_after_clipping { withName: fastqc_after_clipping {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
@ -404,8 +398,6 @@ profiles {
process { process {
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
maxRetries = 2 maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
@ -457,7 +449,7 @@ profiles {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
withName: fastqc_after_clipping { withName: fastqc_after_clipping {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } 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' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }