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nextflow.config
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nextflow.config
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cleanup = true
params {
/*out_dir = './output'*/
report_dir = './reports'
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
try {
includeConfig "${params.custom_config_base}/conf/sanger.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/conf/sanger.config")
}
}
process {
errorStrategy = { task.exitStatus in [130,137..140] ? 'retry' : 'terminate' }
maxRetries = 5
cpus = { 16 * task.attempt }
memory = { 100.GB * task.attempt }
withLabel: single_cpu {cpus = 1}
withLabel: small_mem {memory = 1.GB}
}
profiles {
local {
includeConfig 'conf/local.config'
process.executor = 'local'
}
lsf {
includeConfig 'conf/lsf.config'
}
tower {
enabled = false
accessToken = '[Your-token]'
endpoint = 'http://nf-tower.cellgeni.sanger.ac.uk/api'
}
}
timeline {
enabled = false
file = "${params.report_dir}/timeline.html"
}
trace {
enabled = false
file = 'pipeline_trace.tsv'
sep = '\t'
fields = 'script,env,read_bytes,write_bytes,peak_vmem,peak_rss,vmem,%cpu,%mem,realtime,duration,queue,attempt,memory,disk,cpus,container,module,status,name,hash'
}