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added 1240k profile
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@ -472,4 +472,34 @@ profiles {
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bwaalnl = 16500
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}
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}
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1240k {
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_description = 'nf-core/eager big-data EVA profile provided by nf-core/configs'
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}
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executor {
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queueSize = 6
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}
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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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clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
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// Increasing walltime for bwa to avoid unnecessary retries
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withName:bwa {
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time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 72.h : 48.h }
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}
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withName:markduplicates {
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memory = { task.attempt == 3 ? 16.GB : task.attempt == 2 ? 8.GB : 4.GB }
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}
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}
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}
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}
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