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Merge pull request #334 from jfy133/eva-update

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eva: generalise custom SGE mem flag
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James A. Fellows Yates 2022-03-01 09:23:04 +01:00 committed by GitHub
commit ea052a7b67
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2 changed files with 3 additions and 1 deletions
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2
conf/eva.config
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@ -17,6 +17,7 @@ process {
executor = 'sge' executor = 'sge'
penv = 'smp' penv = 'smp'
queue = 'all.q' queue = 'all.q'
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
} }
executor { executor {
@ -36,6 +37,7 @@ profiles {
process { process {
queue = 'archgen.q' queue = 'archgen.q'
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
} }
singularity { singularity {

2
conf/pipeline/eager/eva.config
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@ -14,7 +14,7 @@ process {
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
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" } clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
withLabel:'sc_tiny'{ withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }