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52 lines
1.6 KiB
Plaintext
52 lines
1.6 KiB
Plaintext
//Profile config names for nf-core/configs
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params {
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config_profile_description = 'National Institutes of Health, USA: Biowulf nf-core config'
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config_profile_contact = 'Kevin Brick (@kevbrick)'
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config_profile_url = 'https://hpc.nih.gov/apps/nextflow.html'
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max_memory = 224.GB
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max_cpus = 32
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max_time = 72.h
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igenomes_base = '/fdb/igenomes/'
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}
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process {
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scratch = '/lscratch/$SLURM_JOBID'
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maxForks = 100
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}
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profiles {
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local {
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process.executor = 'local'
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}
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slurm {
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process.executor = 'slurm'
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executor.$slurm.pollInterval = '1 min'
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executor.$slurm.queueStatInterval = '5 min'
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executor.queueSize = 100
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executor.$slurm.submitRateLimit = '6/1min'
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process.clusterOptions = ' --gres=lscratch:600 --signal USR2@20'
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}
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standard {
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process.executor = 'slurm'
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executor.$slurm.pollInterval = '1 min'
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executor.$slurm.queueStatInterval = '5 min'
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executor.queueSize = 100
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executor.$slurm.submitRateLimit = '6/1min'
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process.clusterOptions = ' --gres=lscratch:600 --signal USR2@20'
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}
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}
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singularity {
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enabled = true
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autoMounts = true
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envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID'
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//As names change, the bind paths required may change too. To chack that everything is being captured:
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//Run '. /usr/local/current/singularity/app_conf/sing_binds' to populate $SINGULARITY_BINDPATH
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//Check that each folder in $SINGULARITY_BINDPATH is listed with -B in the runOptions below. If not, add it.
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runOptions = ' -B /gs10 -B /gs11 -B /gs12 -B /gs4 -B /gs6 -B /gs7 -B /gs8 -B /gs9 -B /vf -B /spin1 -B /data -B /fdb -B /lscratch -B /fdb/igenomes/ --env TMPDIR="/lscratch/$SLURM_JOBID" '
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}
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