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nf-configs/conf/eddie.config

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//Profile config names for nf-core/configs
params {
config_profile_description = 'University of Edinburgh (eddie) cluster profile provided by nf-core/configs.'
config_profile_contact = 'Alison Meynert (@ameynert)'
config_profile_url = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing'
}
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executor {
name = "sge"
queueSize = "100"
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}
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process {
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clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus}" : null }
scratch = true
penv = { task.cpus > 1 ? "sharedmem" : null }
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// common SGE error statuses
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errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
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maxErrors = '-1'
maxRetries = 3
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beforeScript =
"""
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. /etc/profile.d/modules.sh
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sleep 2
module load 'anaconda/5.3.1'
module load 'roslin/singularity/3.5.3'
export SINGULARITY_TMPDIR="\$TMPDIR"
"""
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}
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params {
saveReference = true
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// iGenomes reference base
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igenomes_base = '/exports/igmm/eddie/NextGenResources/igenomes'
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max_memory = 384.GB
max_cpus = 32
max_time = 240.h
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}
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env {
MALLOC_ARENA_MAX=1
}
singularity {
envWhitelist = "SINGULARITY_TMPDIR"
runOptions = '-p'
}