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Merge pull request #382 from jfy133/eva-java-correction
EAGER @ EVA Further Java workarounds
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commit
08435ca300
1 changed files with 15 additions and 23 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_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_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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@ -69,17 +73,17 @@ process {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: fastqc_after_clipping {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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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: adapter_removal {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: bwa {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
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}
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@ -188,26 +192,18 @@ process {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName:get_software_versions {
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cache = false
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clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
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beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" }
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 8)}M" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName:eigenstrat_snp_coverage {
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beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
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}
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withName:kraken_merge {
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beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
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}
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withName:multiqc {
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beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1;'
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clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga() * 2}G" }
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}
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}
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profiles {
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@ -226,8 +222,6 @@ profiles {
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process {
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beforeScript = 'export _JAVA_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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@ -279,7 +273,7 @@ profiles {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: fastqc_after_clipping {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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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@ -404,8 +398,6 @@ profiles {
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process {
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beforeScript = 'export _JAVA_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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@ -457,7 +449,7 @@ profiles {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
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errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
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}
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withName: fastqc_after_clipping {
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clusterOptions = { "-S /bin/bash -V -l h_vmem=${(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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