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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-cmgg/preprocessing Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
// Analysis options
aligner = 'bowtie2'
markdup = 'bamsormadup'
skip_trimming = false
trim_front = 0
trim_tail = 0
adapter_R1 = null
adapter_R2 = null
run_coverage = true
disable_picard_metrics = false
roi = null
genelists = null
// References
genomes = [:]
igenomes_base = '/references'
// igenomes_base = "s3://reference-data/genomes/"
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = "./results"
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
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Schema validation default options
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
includeConfig "${params.custom_config_base}/nfcore_custom.config"
// Load nf-cmgg cluster profiles
includeConfig !System.getenv('NXF_OFFLINE') ? "https://raw.githubusercontent.com/nf-cmgg/configs/main/clusters/cmgg_clusters.config" : "/dev/null"
// Include the igenomes config
includeConfig 'conf/igenomes.config'
// Load nf-cmgg/preprocessing 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/preprocessing.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/preprocessing profiles: ${params.custom_config_base}/pipeline/preprocessing.config")
// }
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.channels = ['conda-forge', 'bioconda']
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
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)'
}
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
apptainer.autoMounts = 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
}
s3_ugent { includeConfig 'conf/profiles/s3_ugent.config' }
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
// analysis profiles
sWGS { includeConfig 'conf/profiles/sWGS.config' }
WGS { includeConfig 'conf/profiles/WGS.config' }
WES { includeConfig 'conf/profiles/WES.config' }
copgt { includeConfig 'conf/profiles/copgt.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 '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf-cmgg/preprocessing custom profiles from different institutions.
// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/preprocessing.config" : "/dev/null"
// 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"
}
// Set bash options
process.shell = """\
bash
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
"""
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
// Enable module binaries by default
nextflow.enable.moduleBinaries = true
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')}.html"
}
manifest {
name = 'nf-cmgg/preprocessing'
author = """CMGG ICT team"""
homePage = 'https://github.com/nf-cmgg/preprocessing'
description = """Demultiplexing, adapter trimming, alignment, and coverage calculation for NGS data."""
mainScript = 'main.nf'
nextflowVersion = '!>=24.10.0'
version = '2.0.4'
doi = ''
}
validation {
defaultIgnoreParams = ["genomes", "igenomes_base"]
help {
enabled = true
command = "nextflow run ${manifest.name} -profile docker --input <samplesheet> --outdir <output_directory>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
beforeText = """
-\033[2m----------------------------------------------------\033[0m-
\033[0;34m ///\033[0;32m/// \033[0m
\033[0;34m ___ __ _ _ __ __ \033[0;34m ///\033[0;32m///// \033[0m
\033[0;34m |\\ | |__ __ / ` | \\/ | / _` / _` \033[0;34m////\033[0;32m////// \033[0m
\033[0;34m | \\| | \\__, | | \\__| \\__| \033[0;34m///\033[0;32m///// \033[0m
\033[0;34m///\033[0;32m/// \033[0m
\033[0;35m ${manifest.name} ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
}
summary {
beforeText = validation.help.beforeText
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'