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nextflow.config
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nextflow.config
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/*
* -------------------------------------------------
* nf-core/neutronstar Nextflow config file
* -------------------------------------------------
* Default config options for all environments.
* Cluster-specific config options should be saved
* in the conf folder and imported under a profile
* name here.
*/
// Global default params, used in configs
params {
outdir = './results'
supernova_container = 'nfcore/supernova:2.1.1'
clusterOptions = false
minsize = 1000
full_output = false
busco_folder = "$baseDir/data"
test = false
reads = false
lanes = false
indices = false
maxreads = false
bcfrac = false
nopreflight = false
no_accept_extreme_coverage = false
genomesize = false
project = false
// Boilerplate options
name = false
multiqc_config = "$baseDir/assets/multiqc_config.yaml"
email = false
email_on_fail = false
maxMultiqcEmailFileSize = 25.MB
plaintext_email = false
monochrome_logs = false
help = false
tracedir = "${params.outdir}/pipeline_info"
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = false
config_profile_contact = false
config_profile_url = false
hostnames = false
}
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag.svg"
}
process.container = 'nfcore/neutronstar:1.0.0'
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
profiles {
conda { process.conda = "$baseDir/environment.yml" }
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
fixOwnership = true
runOptions = "-u \$(id -u):\$(id -g)"
}
singularity { singularity.enabled = true }
test { includeConfig 'conf/test.config' }
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
manifest {
name = 'nf-core/neutronstar'
author = 'Remi-Andre Olsen (@remiolsen)'
homePage = 'https://github.com/nf-core/neutronstar'
description = 'De novo assembly pipeline for 10X linked-reads, used at the SciLifeLab National Genomics Infrastructure.'
mainScript = 'main.nf'
nextflowVersion = '>=19.04.0'
version = '1.0.0'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}