/
nextflow.config
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/
nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
systemsgenetics/entapnf Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
batch_size = 5
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = true
seq_type = "pep"
taxonomy_ID = 2711
// Data files
data_ipr = null
data_nr = null
data_refseq = null
data_sprot = null
data_orthodb = null
data_string = null
data_trembl = null
enzyme_dat = null
skip_entap = false
// Boilerplate options
outdir = './results'
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'link'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,modules'
enable_conda = false
singularity_pull_docker_container = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
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 = '128.GB'
max_cpus = 16
max_time = '240.h'
}
// 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: ${params.custom_config_base}/nfcore_custom.config")
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
// Load systemsgenetics/entapnf custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/entapnf.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/entapnf profiles: ${params.custom_config_base}/pipeline/entapnf.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
}
mamba {
params.enable_conda = true
conda.useMamba = 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
fixOwnership = true
docker.runOptions = "--init"
if (params.data_ipr) {
docker.runOptions += " --volume ${params.data_ipr}:/usr/local/interproscan/data"
}
if (params.data_nr) {
docker.runOptions += " --volume ${params.data_nr}:${params.data_nr}"
}
if (params.data_sprot) {
docker.runOptions += " --volume ${params.data_sprot}:${params.data_sprot}"
}
if (params.data_orthodb) {
docker.runOptions += " --volume ${params.data_orthodb}:${params.data_orthodb}"
}
if (params.data_string) {
docker.runOptions += " --volume ${params.data_string}:${params.data_string}"
}
if (params.data_trembl) {
docker.runOptions += " --volume ${params.data_string}:${params.data_trembl}"
}
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
singularity.runOptions = "-B "
if (params.data_ipr) {
singularity.runOptions += "${params.data_ipr}:/usr/local/interproscan/data,"
}
if (params.data_nr) {
singularity.runOptions += "${params.data_nr}:${params.data_nr},"
}
if (params.data_sprot) {
singularity.runOptions += "${params.data_sprot}:${params.data_sprot},"
}
if (params.data_orthodb) {
singularity.runOptions += "${params.data_orthodb}:${params.data_orthodb},"
}
if (params.data_string) {
singularity.runOptions += "${params.data_string}:${params.data_string},"
}
if (params.data_trembl) {
singularity.runOptions += "${params.data_string}:${params.data_trembl},"
}
singularity.runOptions.replaceFirst(/,$/,'')
}
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
}
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
// 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 = "${params.tracedir}/execution_timeline_${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}.html"
}
manifest {
name = 'systemsgenetics/entapnf'
author = 'Stephen Ficklin, Josh Burns'
homePage = 'https://github.com/systemsgenetics/entapnf'
description = 'EnTAPnf is a workflow that executes the Eukaryotic Non-Model Transcriptome Annotation Pipeline (EnTAP). EnTAP is designed to improve the accuracy, speed, and flexibility of functional gene annotation for both genomes and de novo assembled transcriptomes in non-model eukaryotes.'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
version = '0.1.0'
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
}
}
}