/
nextflow.config
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/
nextflow.config
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//Load params
includeConfig 'conf/params.conf'
//Load process config
includeConfig 'conf/modules.conf'
process {
// TODO nf-core: Check the defaults for all processes
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
maxRetries = 1
maxErrors = '-1'
}
// See https://nextflow-io.github.io/nf-validation/#quick-start
plugins {
id 'nf-validation@0.2.1'
id 'nf-amazon@1.16.2'
}
profiles {
conda {
params.enable_conda = true
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
process.container = 'andreatelatin/denovo:latest'
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
wave {
docker.enabled = true
docker.runOptions = '-u $(id -u):$(id -g)'
wave.enabled = true
wave.strategy = ['conda']
wave.build.conda.basePackages = ['conda-forge::procps-ng']
}
singularity {
process.container = 'docker://andreatelatin/denovo:latest'
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
test_stub_folder {
params.reads = "$baseDir/test-data/mock"
params.outdir = "$baseDir/test-data/results_folder"
stub.enabled = true
}
test_stub_samplesheet {
params.reads = "$baseDir/test-data/samplesheet.csv"
params.outdir = "$baseDir/test-data/results_samplesheet"
stub.enabled = true
}
}
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'telatin/nextflow-example'
author = 'Andrea Telatin, Thanh Le-Viet'
homePage = 'https://github.com/telatin/nextflow-example'
description = 'A Small Assembly Pipeline'
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.0'
}
// 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
}
}
}