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moving executor outside of process
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so that is is more clear to be able to reuse in profile
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Qi Yu committed Jun 7, 2024
1 parent a1b4492 commit c77c117
Showing 1 changed file with 8 additions and 8 deletions.
16 changes: 8 additions & 8 deletions conf/biowulf.config
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,6 @@ params {
config_profile_description = 'Biowulf nf-core config'
config_profile_contact = '[email protected]'
config_profile_url = 'https://hpc.nih.gov/apps/nextflow.html'
max_memory = '224 GB'
max_cpus = 32
max_time = '72 h'
clusterOptions = null
igenomes_base = '/fdb/igenomes_nf/'
}
Expand All @@ -24,21 +21,24 @@ env {
OPENBLAS_NUM_THREADS = 1
}


process {
executor = 'slurm'
maxRetries = 1
executor {
name = 'slurm'
queue = 'norm'
queueSize = 200
pollInterval = '2 min'
queueStatInterval = '5 min'
submitRateLimit = '6/1min'
retry.maxAttempts = 1

clusterOptions = ' --gres=lscratch:200 '
scratch = '/lscratch/$SLURM_JOB_ID'
}

process {
executor = 'slurm'
maxRetries = 1
stageInMode = 'symlink'
stageOutMode = 'rsync'
resourceLimits = [ cpus: 128, memory: 499.GB, time: 240.h ]
// for running pipeline on group sharing data directory, this can avoid inconsistent files timestamps
cache = 'lenient'
}
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