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Merge pull request #113 from jfy133/master

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Updates SHH specific nf-core/eager pipeline
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James A. Fellows Yates 2019-12-21 22:28:38 +01:00 committed by GitHub
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2 changed files with 4 additions and 3 deletions
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5
conf/pipeline/eager/shh.config
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@ -10,8 +10,9 @@ params {
// Specific nf-core/eager process configuration // Specific nf-core/eager process configuration
process { process {
withName: malt { withName: malt {
memory = { 725.GB * task.attempt } maxRetries = 1
cpus = { 64 * task.attempt } memory = { task.attempt > 1 ? 1900.GB : 725.GB }
cpus = { task.attempt > 1 ? 112 : 64 }
time = 1440.h time = 1440.h
queue = { task.memory > 756.GB ? 'supercruncher' : 'long' } queue = { task.memory > 756.GB ? 'supercruncher' : 'long' }
} }

2
docs/pipeline/eager/shh.md
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@ -14,4 +14,4 @@ Example: `nextflow run nf-core/eager -profile shh`
Specific configurations for shh has been made for eager. Specific configurations for shh has been made for eager.
* Running with the MALT module turned on, will by default be sent either to long or supercruncher queues with a minimum of 756GB and 64 cores. * If running with the MALT module turned on, the MALT process by default will be sent to the long queue with a resource requirement minimum of 725GB and 64 cores. If this fails, the process will be tried once more only and sent to the supercruncher queue. The module will not retry after this, and pipeline will fail.