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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MDL/metabolt Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// MDL/metabolt: Specify the pipeline's command line flags
// Input options
input = null
// FASTP - preprocessing options
adapter_fasta = null // path to adapter fasta file, or null if not used
discard_trimmed_pass = false
save_trimmed_fail = false
save_merged = false
// (ext.args defined in nextflow.config)
fastp_phred_quality = 20
reads_minlength = 70
trim_front_bases = 10
trim_tail_bases = 10
deduplication = true
// MEGAHIT - assembly options
megahit_kmer_list = "31,59,87,115,143"
megahit_min_contig_len = 1500
// METABAT2 - binning options
metabat2_min_contig_len = 1500
metabat2_seed = 9999
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false
// 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
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
help_full = false
show_hidden = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
// 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'
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
}
wave {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
wave.enabled = true
wave.freeze = true
wave.strategy = 'conda,container'
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load MDL/metabolt custom profiles from different institutions.
// Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
charliecloud.registry = 'quay.io'
// Load igenomes.config if required
includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Set bash options
process.shell = [
"bash",
"-C", // No clobber - prevent output redirection from overwriting files.
"-e", // Exit if a tool returns a non-zero status/exit code
"-u", // Treat unset variables and parameters as an error
"-o pipefail" // Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
]
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${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 = 'MDL/metabolt'
author = """Muhammad Muneeb Nasir"""
homePage = 'https://github.com/muneebdev7/metabolt'
description = """Lightning fast & automated metagenomic pipeline powered by Nextflow"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.04.2'
version = '0.6.1'
doi = ''
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
id '[email protected]' // Measures CO2 foot-print to run the pipeline - HTML report
}
validation {
defaultIgnoreParams = ["genomes"]
help {
enabled = true
command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
beforeText = """
\033[0;34m__| |_____________________________________________________________________________| |__\033[0m
\033[0;34m__ _____________________________________________________________________________ __\033[0m
\033[0;34m | | | |\033[0m
\033[0;34m | |\033[0m \033[0;32m__ __ ____ _ __ _ ____ _ _ _\033[0m \033[0;34m| |\033[0m
\033[0;34m | |\033[0m \033[0;32m| \\/ | _ \\| | / / _ __ ___ ___| |_ __ _| __ ) ___ | | |_ | |\033[0m \033[0;34m| |\033[0m
\033[0;34m | |\033[0m \033[0;32m| |\\/| | | | | | / / | '_ ` _ \\ / _ \\ __/ _` | _ \\ / _ \\| | __| | |\033[0m \033[0;34m| |\033[0m
\033[0;34m | |\033[0m \033[0;32m| | | | |_| | |___ / / | | | | | | __/ || (_| | |_) | (_) | | |_ |_|\033[0m \033[0;34m| |\033[0m
\033[0;34m | |\033[0m \033[0;32m|_| |_|____/|_____| /_/ |_| |_| |_|\\___|\\__\\__,_|____/ \\___/|_|\\__| (_)\033[0m \033[0;34m| |\033[0m
\033[0;34m | | | |\033[0m
\033[0;34m | | -. .-. .-. .-. .-. .-. . | |\033[0m
\033[0;34m | | ||\\|||\\ /|||\\|||\\ /|||\\|||\\ /| | |\033[0m
\033[0;34m | | |/ \\|||\\|||/ \\|||\\|||/ \\|||\\|| | |\033[0m
\033[0;34m | | ~ `-~ `-` `-~ `-` `-~ `- | |\033[0m
\033[0;34m | | | |\033[0m
\033[0;34m | | \033[0;35m${manifest.name} ${manifest.version}\033[0m \033[0;34m| |\033[0m
\033[0;34m__| |_____________________________________________________________________________| |__\033[0m
\033[0;34m__ _____________________________________________________________________________ __\033[0m
\033[0;34m | | | |\033[0m
"""
}
summary {
beforeText = validation.help.beforeText
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'