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so that is is more clear to be able to reuse in profile
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Qi Yu
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Jun 7, 2024
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@@ -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/' | ||
} | ||
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@@ -24,21 +21,24 @@ env { | |
OPENBLAS_NUM_THREADS = 1 | ||
} | ||
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process { | ||
executor = 'slurm' | ||
maxRetries = 1 | ||
executor { | ||
name = 'slurm' | ||
queue = 'norm' | ||
queueSize = 200 | ||
pollInterval = '2 min' | ||
queueStatInterval = '5 min' | ||
submitRateLimit = '6/1min' | ||
retry.maxAttempts = 1 | ||
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clusterOptions = ' --gres=lscratch:200 ' | ||
scratch = '/lscratch/$SLURM_JOB_ID' | ||
} | ||
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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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