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https://github.com/MillironX/nf-configs.git
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58 lines
1.2 KiB
Text
58 lines
1.2 KiB
Text
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Sheffield Bioinformatics Core Configuration Profile - ShARC
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Base Institutional Configuration
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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params {
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// nf-core specific parameters displayed in header summary of each run
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config_profile_description = 'Sheffield Bioinformatics Core - ShARC'
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config_profile_contact = 'Lewis Quayle (l.quayle@sheffield.ac.uk)'
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config_profile_url = 'https://docs.hpc.shef.ac.uk/en/latest/sharc/index.html'
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// hpc resource limits
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max_cpus = 16
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max_memory = 64.GB
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max_time = 96.h
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}
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// container engine
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singularity {
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enabled = true
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autoMounts = true
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}
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// hpc configuration specific to ShARC
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process {
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// scheduler
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executor = 'sge'
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penv = 'smp'
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queue = { task.time <= 6.h ? 'shortint.q' : 'all.q' }
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clusterOptions = { "-l rmem=${task.memory.toGiga()}G" }
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// error and retry handling
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errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' }
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maxRetries = 2
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}
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