/*
========================================================================================
ARETE Nextflow config file
========================================================================================
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input_sample_table = null
// Database cache
db_cache = null
// PopPunk
skip_poppunk = false
poppunk_model = null
run_poppunk_qc = false
// Subsampling parameters
enable_subsetting = false
core_similarity = 99.9
accessory_similarity = 99
// Phylogenomics parameters
skip_phylo = false
use_ppanggolin = false
use_full_alignment = false
use_fasttree = true
// Annotation parameters
use_prokka = false
bakta_db = null
annotation_tools = 'mobsuite,rgi,cazy,vfdb,iceberg,bacmet,islandpath,phispy,report'
feature_profile_columns = 'mobsuite,rgi,cazy,vfdb,iceberg,bacmet'
feature_dispersion_columns = null
upset_plot_columns = null
min_pident = 60
min_qcover = 0.6
skip_profile_creation = false
// References
reference_genome = null
// Kraken2
skip_kraken = false
// Gene Order
run_gene_order = false
input_file_path = "$projectDir/test/gene-order/rgi_input.txt"
gene_order_percent_cutoff = 0.25
gene_order_label_cols = null
num_neighbors = 10
// Optional clustering module hyperparameter options
inflation = 2
epsilon = 0.5
minpts = 5
plot_clustering = false
// QC options
run_checkm = false
apply_filtering = false
min_n50 = 10000
min_contigs_1000_bp = 1
min_contig_length = 1
// Recombination
run_recombination = false
run_verticall = true
run_gubbins = false
// Dynamics
run_evolccm = false
run_rspr = false
min_rspr_distance = 10
min_branch_length = 0
max_support_threshold = 0.7
max_approx_rspr = -1
min_heatmap_approx_rspr = 0
max_heatmap_approx_rspr = -1
min_heatmap_exact_rspr = 0
max_heatmap_exact_rspr = -1
// rSPR/evolCCM entries
core_gene_tree = null
concatenated_annotation = null
feature_profile = null
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = "$projectDir/assets/arete-logo-transparent.png"
max_multiqc_email_size = '25.MB'
// Boilerplate options
outdir = './results'
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,modules'
enable_conda = false
singularity_pull_docker_container = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = [:]
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '125.GB'
max_cpus = 72
max_time = '168.h'
}
// 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")
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
light { includeConfig 'conf/light.config' }
small { includeConfig 'conf/base.config' }
medium { includeConfig 'conf/medium.config' }
large { includeConfig 'conf/large.config' }
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
}
manifest {
name = 'beiko-lab/ARETE'
author = 'Finlay Maguire'
homePage = 'https://github.com/beiko-lab/arete'
description = 'AMR/VF LGT-focused bacterial genomics workflow'
mainScript = 'main.nf'
nextflowVersion = '!>=22.10.6'
version = '1.0.1'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}