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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/variantbenchmarking Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
outdir = null
// Option to select analysis type: germline or somatic
analysis = null
// Option to select variant type to analysis: small, snv, indel, somatic, copynumber
variant_type = null
// Truth parameters
truth_id = null
truth_vcf = null
regions_bed = null
// Benchmarking method
method = 'truvari,svanalyzer,happy,rtgtools,wittyer,sompy,intersect'
// Preprocess spesific parameters
preprocess = ""
sv_standardization = ""
// Filtering parameters
min_sv_size = 0
max_sv_size = -1
min_allele_freq = -1
min_num_reads = -1
// use bcftools expressions https://samtools.github.io/bcftools/bcftools.html#expressions together with variant_filtering parameter!
include_expression = null
exclude_expression = null
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false
sdf = null
dictionary = null
rename_chr = null
chain = null
liftover = ""
// 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
monochromeLogs = 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/'
trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// 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
test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/variantbenchmarking'
// 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
}
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
process {
resourceLimits = [
memory: 8.GB,
cpus : 4,
time : 1.h
]
}
}
test { includeConfig 'conf/test.config' }
germline_small { includeConfig 'conf/tests/germline_small.config' }
germline_sv { includeConfig 'conf/tests/germline_sv.config' }
somatic_snv { includeConfig 'conf/tests/somatic_snv.config' }
somatic_indel { includeConfig 'conf/tests/somatic_indel.config' }
somatic_sv { includeConfig 'conf/tests/somatic_sv.config' }
somatic_cnv { includeConfig 'conf/tests/somatic_cnv.config' }
liftover_test { includeConfig 'conf/tests/liftover_test.config' }
liftover_truth { includeConfig 'conf/tests/liftover_truth.config' }
test_full { includeConfig 'conf/test_full.config' }
test_somatic_full { includeConfig 'conf/test_full_somatic.config' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf-core/variantbenchmarking custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/variantbenchmarking.config" : "/dev/null"
// 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", // Returns the status of the last command to exit..
"pipefail" // ..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
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}
prov {
enabled = true
formats {
bco {
file = "${params.outdir}/pipeline_info/manifest_${params.trace_report_suffix}.bco.json"
}
}
}
manifest {
name = 'nf-core/variantbenchmarking'
author = """[email protected]""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
contributors = [
[
name: 'Kuebra Narci',
affiliation: 'GHGA',
email: '[email protected]',
github: '@kubranarci',
contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: '0000-0002-3532-2152'
]
]
homePage = 'https://github.com/nf-core/variantbenchmarking'
description = """Variant Benchmarking pipeline for germline and somatic variant callers """
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=24.04.2'
version = '1.1.0'
doi = '110.5281/zenodo.14916661'
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
id '[email protected]' // Provenance reports for pipeline runs
}
validation {
defaultIgnoreParams = ["genomes"]
monochromeLogs = params.monochrome_logs
help {
enabled = true
command = "nextflow run nf-core/variantbenchmarking -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
beforeText = """
-\033[2m----------------------------------------------------\033[0m-
\033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m
\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m
\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m
\033[0;32m`._,._,\'\033[0m
\033[0;35m nf-core/variantbenchmarking ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/variantbenchmarking/blob/master/CITATIONS.md
"""
}
summary {
beforeText = validation.help.beforeText
afterText = validation.help.afterText
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'