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nextflow.config
executable file
·52 lines (47 loc) · 1.48 KB
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nextflow.config
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params {
manifest = ""
results_dir = ""
db_dir = "./db"
gps_db_name = "GPS_v6"
gps_db = "https://gps-project.cog.sanger.ac.uk/${gps_db_name}.zip"
gps_db_local = "${db_dir}/${gps_db_name}"
}
profiles {
standard {
process {
memory = "8GB"
cpus = 2
}
docker {
enabled = true
runOptions = '-u $(id -u):$(id -g)'
}
}
farm {
docker {
enabled = false
}
singularity {
enabled = true
autoMounts = true
cacheDir = "$PWD"
}
process {
cpus = 1
memory = "8GB"
errorStrategy = {task.attempt <= 0 ? 'retry' : 'ignore'}
maxRetries = 0
withName:get_GPSC {
memory = '8000 MB'
cpus = 4
queue = 'normal'
}
}
executor {
name = "lsf"
perJobMemLimit = true
jobName = { "gpcs_pipeline - $task.name - $task.hash" }
pollInterval = "5 sec"
}
}
}