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nextflow.config
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nextflow.config
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docker.enabled = true
manifest {
name = 'qcflow'
description = 'Perform qc on illumina reads'
homePage = 'https://github.com/darcyabjones/qcflow'
author = 'Darcy Jones'
mainScript = 'main.nf'
nextflowVersion = '>=0.31.1'
version = "0.0.1"
}
params {
max_memory = 48.GB
max_cpus = 16
max_time = 24.h
help = false
tracedir = "trace"
outdir = "."
}
profiles {
standard {
includeConfig "conf/base.config"
}
pawsey_zeus {
includeConfig "conf/pawsey_zeus.conf"
}
pawsey_magnus {
includeConfig "conf/pawsey_magnus.conf"
}
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = true
file = "${params.tracedir}/pipeline_info/pclust_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/pipeline_info/pclust_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/pipeline_info/pclust_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_info/pclust_DAG.svg"
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
// From NFCORE
def check_max(obj, type) {
if(type == 'memory'){
try {
if(obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if(type == 'time'){
try {
if(obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if(type == 'cpus'){
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}