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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
fastq = null
flowcell = null
bam = null
cram = null
// Trimming options
skip_trimming = false
trim_front = 0
trim_tail = 0
adapter_R1 = null
adapter_R2 = null
// Alignment options
aligner = "bowtie2"
markdup = "bamsormadup"
// Coverage analysis option
run_coverage = false
target_regions = null
// Pipeline options
// set `ext.when` for picard in `modules.config`
disable_picard_metrics = true
// References
genome = "GRCh38"
genomes_base = "/references"
genomes_ignore = false
igenomes_base = "s3://reference-data/genomes"
igenomes_ignore = true
// MultiQC options
multiqc_config = null
multiqc_logo = "${projectDir}/assets/CMGG_logo.png"
multiqc_title = null
max_multiqc_email_size = "25.MB"
multiqc_methods_description = null
// Boilerplate options
outdir = "output"
publish_dir_mode = "copy"
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = System.getenv('HOOK_URL')
help = false
version = false
// Config options
cmgg_config_version = "main"
cmgg_config_base = "https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-configs/${params.cmgg_config_version}"
config_profile_name = null
config_profile_description = null
custom_config_version = "master"
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = "88.GB"
max_cpus = 36
max_time = "72.h"
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes'
validationShowHiddenParams = false
validate_params = true
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig "conf/base.config"
// Load modules.config for DSL2 module specific options
includeConfig "conf/modules.config"
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/nf-cmgg-preprocessing.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/nf-cmgg-preprocessing profiles: ${params.custom_config_base}/pipeline/nf-cmgg-preprocessing.config")
// }
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
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
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
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
}
nomad { includeConfig "conf/profiles/nomad.config" }
cmgg { includeConfig "conf/profiles/cmgg.config" }
"coPGT-M" { includeConfig "conf/profiles/coPGT-M.config" }
SeqCap { includeConfig "conf/profiles/SeqCap.config" }
WES { includeConfig "conf/profiles/WES.config" }
WGS { includeConfig "conf/profiles/WGS.config" }
sWGS { includeConfig "conf/profiles/sWGS.config" }
nftest { includeConfig "conf/test/nftest.config" }
test { includeConfig "conf/test/test.config" }
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
// Nextflow plugins
plugins {
id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig "conf/genomes/igenomes.config"
} else if (!params.genomes_ignore){
includeConfig "conf/genomes/genomes.config"
} else {
params.genomes = [:]
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages 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"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
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
overwrite = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
overwrite = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing'
author = """matthdsm"""
homePage = 'https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing'
description = """Preprocessing workflow for sequencing data at CMGG"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.2.0'
doi = ''
}
// 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
}
}
}