forked from nf-core/hic
/
nextflow.config
139 lines (126 loc) · 3.83 KB
/
nextflow.config
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/*
* -------------------------------------------------
* nf-core/hic Nextflow config file
* -------------------------------------------------
* Default config options for all environments.
*/
// Global default params, used in configs
params {
// Workflow flags
// Specify your pipeline's command line flags
reads = "*{1,2}.fastq.gz"
outdir = './results'
genome = false
readPaths = false
chromosome_size = false
restriction_fragments = false
skipMaps = false
skipIce = false
skipCool = false
skipMultiQC = false
dnase = false
// Boilerplate options
name = false
multiqc_config = "$baseDir/assets/multiqc_config.yaml"
email = false
maxMultiqcEmailFileSize = 25.MB
plaintext_email = false
monochrome_logs = false
help = false
igenomes_base = "./iGenomes"
tracedir = "${params.outdir}/pipeline_info"
awsqueue = false
awsregion = 'eu-west-1'
igenomesIgnore = false
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = false
config_profile_description = false
config_profile_contact = false
config_profile_url = false
}
// Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev
process.container = 'nfcore/hic:dev'
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load hic config file
includeConfig 'conf/hicpro.config'
// Create profiles
profiles {
awsbatch { includeConfig 'conf/awsbatch.config' }
conda { process.conda = "$baseDir/environment.yml" }
debug { process.beforeScript = 'echo $HOSTNAME' }
docker { docker.enabled = true }
singularity { singularity.enabled = true }
test { includeConfig 'conf/test.config' }
}
// Load igenomes.config if required
if(!params.igenomesIgnore){
includeConfig 'conf/igenomes.config'
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = true
file = "${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 = "${params.tracedir}/pipeline_dag.svg"
}
manifest {
name = 'nf-core/hic'
author = 'Nicolas Servant'
homePage = 'https://github.com/nf-core/hic'
description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
mainScript = 'main.nf'
nextflowVersion = '>=19.04.0'
version = '1.1.1dev'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if(type == 'memory'){
try {
if(obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}