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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/pathogensurveillance Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
reference_data = null
bakta_db = null
temp_dir = null
data_dir = 'path_surveil_data'
download_bakta_db = true
max_depth = 100
only_latin_binomial_refs = false
allow_non_refseq = false
allow_atypical_refs = false
allow_unannotated = false
n_ref_strains = 5
n_ref_species = 20
n_ref_genera = 10
n_ref_closest = 2
n_ref_closest_named = 1
n_ref_context = 5
ref_min_ani = 0.95
phylo_min_genes = 30
phylo_max_genes = 300
bakta_db_type = 'light'
// 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'
copymode = 'medium'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
help_full = false
validate_params = true
show_hidden_params = false
hpc_queue = null
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
config_profile_name = null
// Max total options for all jobs combined
max_total_memory = null
max_total_cpus = null
max_total_jobs = null
// Schema validation default options
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
executor.cpus = params.max_total_cpus
executor.memory = params.max_total_memory
executor.queueSize = params.max_total_jobs
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)'
}
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
]
}
}
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' }
testserratia_38 { includeConfig 'conf/testserratia_38.config' }
serratia_N664 { includeConfig 'conf/serratia_N664.config'}
small_genome { includeConfig 'conf/small_genome.config' }
salmonella { includeConfig 'conf/salmonella.config' }
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf-core/pathogensurveillance custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/pathogensurveillance.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'
// 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"
}
manifest {
name = 'nf-core/pathogensurveillance'
author = """Zachary S.L. Foster, Camilo Parada-Rojas, Logan Blair, Martha Sudermann, Nicholas C. Cauldron, Fernanda I. Bocardo, Ricardo Alcalá-Briseño, Hung Phan, Jeff H. Chang, Niklaus J. Grünwald"""
contributors = [
// TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
[
name: 'Zachary S.L. Foster',
affiliation: '',
email: '',
github: '',
contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: ''
],
[
name: ' Martha Sudermann',
affiliation: '',
email: '',
github: '',
contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: ''
],
[
name: ' Nicholas C. Cauldron',
affiliation: '',
email: '',
github: '',
contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: ''
],
[
name: ' Fernanda I. Bocardo',
affiliation: '',
email: '',
github: '',
contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: ''
],
[
name: ' Hung Phan',
affiliation: '',
email: '',
github: '',
contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: ''
],
[
name: ' Jeff H. Chang',
affiliation: '',
email: '',
github: '',
contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: ''
],
[
name: ' Niklaus J. Grünwald',
affiliation: '',
email: '',
github: '',
contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: ''
],
]
homePage = 'https://github.com/nf-core/pathogensurveillance'
description = """Surveillance of pathogens using high-throughput sequencing"""
mainScript = 'main.nf'
defaultBranch = 'main'
nextflowVersion = '!>=24.04.2'
version = '1.0.0'
doi = ''
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
defaultIgnoreParams = ["genomes"]
monochromeLogs = params.monochrome_logs
help {
enabled = true
command = "nextflow run nf-core/pathogensurveillance -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/pathogensurveillance ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${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/pathogensurveillance/blob/main/CITATIONS.md
"""
}
summary {
beforeText = validation.help.beforeText
afterText = validation.help.afterText
}
}
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'
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'