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nextflow.config
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/*
* -------------------------------------------------
* 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.
*/
manifest {
homePage = 'https://github.com/BU-ISCIII/bacterial_wgs_training'
description = 'This is a project for wgs analysis trainning using nextflow and containers.'
mainScript = 'main.nf'
}
// Global default params, used in configs
params {
ver = '1.0' //Pipeline version
nf_required_version = '0.27.6' //Minimum version of Nextflow required
reads="$baseDir/data/samples/*.fastq"
outdir='results'
}
profiles {
standard {
includeConfig 'conf/base.config'
}
docker {
includeConfig 'conf/docker.config'
}
singularity {
includeConfig 'conf/singularity.config'
}
hpc_isciii {
// TODO. with modules.
}
testing {
// TODO
}
aws {
// TO DO
}
none {
// Don't load any config (for use with custom home configs)
}
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
// By default output execution reports
timeline {
enabled = true
file = "${params.outdir}/timeline.html"
}
report {
enabled = true
file = "${params.outdir}/report.html"
}
trace {
enabled = true
file = "${params.outdir}/trace.txt"
}
dag {
enabled = true
file = "${params.outdir}/DAG.svg"
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
//def check_max(obj, type) {
// if(type == 'memory'){
// if(obj.compareTo(params.max_memory) == 1)
// return params.max_memory
// else
// return obj
// } else if(type == 'time'){
// if(obj.compareTo(params.max_time) == 1)
// return params.max_time
// else
// return obj
// } else if(type == 'cpus'){
// return Math.min( obj, params.max_cpus )
// }
//}