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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/plantpathsurveil Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
sample_data = null
reference_data = null
bakta_db = null
temp_dir = null
data_dir = 'path_surveil_data'
download_bakta_db = false
max_depth = 100
n_ref_strains = 30
n_ref_species = 20
n_ref_genera = 10
n_ref_closest = 3
n_ref_context = 5
ref_min_ani = 0.8
phylo_min_genes = 10
phylo_max_genes = 100
bakta_db_type = 'light'
cache_type = 'true'
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
out_dir = null
trace_dir = "${params.out_dir}/pipeline_info"
publish_dir_mode = 'copy'
copymode = 'medium'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
enable_conda = false
hpc_queue = null
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options for individual jobs
// Defaults only, expecting to be overwritten
max_memory = '64.GB'
max_cpus = 16
max_time = '240.h'
// Max total options for all jobs combined
max_total_memory = null
max_total_cpus = null
max_total_jobs = null
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.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: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/plantpathsurveil custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/plantpathsurveil.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/plantpathsurveil profiles: ${params.custom_config_base}/pipeline/plantpathsurveil.config")
// }
executor.cpus = params.max_total_cpus
executor.memory = params.max_total_memory
executor.queueSize = params.max_total_jobs
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
conda.enabled = true
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
mamba {
conda.enabled = true
params.enable_conda = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.registry = 'quay.io'
docker.enabled = true
docker.runOptions = '-u $(id -u):$(id -g)' // replaces the depreciated 'docker.userEmulation' option
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
}
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
}
slurm {
executor.name = 'slurm' // Use SLURM for job scheduling
executor.memory = 200.GB
process.queue = params.hpc_queue // SLURM partition
executor.clusterOptions = '--qos=normal' // Additional SLURM options
executor.perCpuMemAllocation = false // Enable per-CPU memory allocation if required by the cluster
}
xanthomonas { includeConfig 'conf/xanthomonas.config' }
xanthomonas_small { includeConfig 'conf/xanthomonas_small.config' }
ramorum_small { includeConfig 'conf/ramorum_small.config' }
mixed { includeConfig 'conf/mixed.config' }
mixed_bacteria { includeConfig 'conf/mixed_bacteria.config' }
mycobacteroides { includeConfig 'conf/mycobacteroides.config' }
mycobacteroides_small { includeConfig 'conf/mycobacteroides_small.config' }
high_complexity_kpneumoniae { includeConfig 'conf/high_complexity_kpneumoniae.config' }
wagner_2023 { includeConfig 'conf/wagner_2023.config' }
wagner_2023_small { includeConfig 'conf/wagner_2023_small.config' }
chaos { includeConfig 'conf/chaos.config' }
aps_workshop { includeConfig 'conf/aps_workshop.config' }
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
ppluvialis { includeConfig 'conf/ppluvialis.config' }
complex_small { includeConfig 'conf/complex_small.config' }
complex_minimal { includeConfig 'conf/complex_minimal.config' }
complex { includeConfig 'conf/complex.config' }
cqls { includeConfig 'conf/cqls.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"
}
// 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 = "${params.trace_dir}/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.trace_dir}/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.trace_dir}/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.trace_dir}/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'nf-core/plantpathsurveil'
author = 'Zachary S.L. Foster, Martha Sudermann, Nicholas C. Cauldron, Fernanda I. Bocardo, Hung Phan, Jeff H. Chang, Niklaus J. Grünwald'
homePage = 'https://github.com/nf-core/plantpathsurveil'
description = 'Surveillance of plant pathogens using high-throughput sequencing'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
version = '1.0dev'
doi = ''
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// 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
}
}
}
def check_prio(copymode_level, copy_priority) {
if (copymode_level == 'high') {
return 'copy'
} else if (copymode_level == 'medium' && copy_priority != 'low') {
return 'copy'
} else {
return 'symlink'
}
}