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50 lines
1.2 KiB
Text
50 lines
1.2 KiB
Text
//Profile config names for nf-core/configs
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params {
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config_profile_description = 'University of Edinburgh (eddie) cluster profile provided by nf-core/configs.'
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config_profile_contact = 'Alison Meynert (@ameynert)'
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config_profile_url = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing'
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}
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executor {
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name = "sge"
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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 }
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scratch = true
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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'
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maxRetries = 3
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beforeScript =
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"""
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. /etc/profile.d/modules.sh
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module load 'roslin/singularity/3.5.3'
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export SINGULARITY_TMPDIR="\$TMPDIR"
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"""
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}
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params {
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saveReference = true
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// iGenomes reference base
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igenomes_base = '/exports/igmm/eddie/BioinformaticsResources/igenomes'
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max_memory = 384.GB
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max_cpus = 32
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max_time = 240.h
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}
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env {
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MALLOC_ARENA_MAX=1
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}
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singularity {
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envWhitelist = "SINGULARITY_TMPDIR,TMPDIR"
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runOptions = '-p -B "$TMPDIR"'
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enabled = true
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autoMounts = true
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}
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