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nextflow.config
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// *****************
// Autometa Nextflow Configuration
// Default config options for all compute environments
// *****************
manifest {
name = "autometa"
author = "Jason C. Kwan Lab"
homePage = "https://github.com/KwanLab/Autometa"
defaultBranch = "main"
description = "Autometa: Automated Extraction of Microbial Genomes from Shotgun Metagenomes"
doi = "https://doi.org/10.1093/nar/gkz148"
mainScript = "main.nf"
nextflowVersion = ">=21.04.0"
version = "2.2.3"
}
// Global default params, used in configs
params {
/*
* -------------------------------------------------
* Change runtime
* -------------------------------------------------
*/
use_run_name = false
debug = false
mock_test = false
autometa_image_tag = manifest.version //default docker image version is same as version in manifest, above
/*
* -------------------------------------------------
* Parallelization
* -------------------------------------------------
*/
// Input options
input = null // samplesheet path (.csv)
outdir = "autometa-nxf-output"
/*
* -------------------------------------------------
* Taxonomy-aware data subsetting
* -------------------------------------------------
*/
taxonomy_aware = false
single_db_dir = null
nr_dmnd_dir = null
prot_accession2taxid_gz_dir = null
taxdump_tar_gz_dir = null
large_downloads_permission = false
binning_starting_rank = "superkingdom" // choices: "superkingdom", "phylum", "class", "order", "family", "genus", "species"
/*
* -------------------------------------------------
* Binning Parameters
* -------------------------------------------------
*/
length_cutoff = 3000
kmer_size = 5
norm_method = "am_clr"
pca_dimensions = 50
embedding_method = "bhsne"
embedding_dimensions = 2
kingdom = "bacteria"
clustering_method = "dbscan"
classification_method = "decision_tree"
classification_kmer_pca_dimensions = 50
completeness = 20.0
purity = 90.0
gc_stddev_limit = 25.0
cov_stddev_limit = 5.0
unclustered_recruitment = false
/*
* -------------------------------------------------
* Boilerplate options
* -------------------------------------------------
*/
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = null
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = null
schema_ignore_params = 'genomes,modules'
enable_conda = false
singularity_pull_docker_container = null
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = [:]
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '16.GB'
max_cpus = 4
max_time = '240.h'
}
params.tracedir = "${params.outdir}/trace"
// 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 $HOSTNAME' }
standard {
process.executor = "local"
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
slurm {
process.executor = "slurm"
// NOTE: You can determine your slurm partition (e.g. process.queue) with the `sinfo` command
process.queue = "queue"
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
executor {
queueSize = 8
}
}
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/trace/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/trace/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/trace/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/trace/pipeline_dag_${trace_timestamp}.svg"
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}