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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mira-nf/mira Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
Will go back and cut out what is not needed upon completion of pipeline
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
//MIRA options
input = null
runpath = null
e = null
p = null
custom_primers = null
process_q = null
reformat_tables = false
subsample_reads = 0
irma_module = 'none'
custom_irma_config = null
custom_qc_settings = null
amd_platform = false
sourcepath = null
read_qc = false
ecr_registry = null
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
monochrome_logs = false
hook_url = null
help = false
version = null
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = false
validationShowHiddenParams = false
validate_params = true
}
/*
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load mira-nf/mira custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/mira.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/mira profiles: ${params.custom_config_base}/pipeline/mira.config")
// }
*/
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = false
}
docker {
docker.enabled = false
conda.enabled = false
singularity.enabled = true
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
// Set cache directory for Singularity images.
singularity.cacheDir = "$HOME/singularityIMG"
// Prevents mounting errors in Singularity container creation caused by bad TMPDIR creation.
process {
scratch = false
}
}
podman {
podman.enabled = false
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = false
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = false
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = false
apptainer.autoMounts = false
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
sge {
// Disable docker by default
docker.enabled = false
// Load configs
includeConfig 'conf/base.config'
includeConfig 'conf/modules.config'
executor {
name = 'sge'
queueSize = 16
pollInterval = '10sec'
submitRateLimit = '2sec'
}
process {
// Executor information
executor = 'sge'
jobName = { "$task.name - $task.hash" }
penv = 'smp'
queue = "${params.process_q}"
}
}
slurm {
// Load configs
includeConfig 'conf/base.config'
includeConfig 'conf/modules.config'
process.executor = 'slurm'
executor.queueSize = 16
executor.perCpuMemAllocation = true
singularity.runOptions = '--bind /scratch:/scratch'
cleanup = true
}
local {
// Disable docker by default
docker.enabled = false
// Load local_base.config and modules
includeConfig 'conf/local_base.config'
includeConfig 'conf/modules.config'
}
standard {
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
includeConfig 'conf/omics.config'
}
test { includeConfig 'conf/test.config' }
//test_full { includeConfig 'conf/test_full.config' }
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
id '[email protected]' // For paramsSummaryMap
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
// Sets options for the Java runtime instance.
NFX_OPTS="-Xms=512m -Xmx=8g"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
// Resources - expected to be overwritten
process.memory = '5.GB'
process.cpus = 1
process.time = '72.h'
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
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 = 'mira-nf/mira'
author = """Ben Rambo-Martin, Kristine Lacek, Reina Chau, Amanda Sullivan"""
homePage = 'https://github.com/mira-nf/mira'
description = """Pipeline for Influenza, SARS-CoV-2, and RSV genome assembly, annotation, and curation"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.0.0'
doi = ''
}
// Load modules.config for DSL2 module specific options
// 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
}
}
}