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nextflow.config
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nextflow.config
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/*
========================================================================================
cdc/phoenix Nextflow conf-core schema lint nextflow_schema.jsonnfig file
========================================================================================
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input and Output options
input = null
outdir = "${PWD}/results"
kraken2db = null
busco_db_path = null
// Params for Filtering
minlength = 500
phred = 33
//SRA mandatory please do not remove
results = "${baseDir}/results/fastq_files"
new_samplesheet = "${baseDir}/assets/sra_samples.csv"
// Terra specific options
terra = false
// Database paths
//path2db = "${baseDir}/assets/databases" // need this for kraken2db if you place those files in the assets folder
placeholder = "${baseDir}/assets/placeholder.txt" // need for passing empty line to spades
bbdukdb = "${baseDir}/assets/databases/phiX.fasta"
zipped_sketch = "${baseDir}/assets/databases/REFSEQ_20220915_Bacteria_complete.msh.gz"
ncbi_assembly_stats = "${baseDir}/assets/databases/NCBI_Assembly_stats_20220928.txt"
taxa = "${baseDir}/assets/databases/taxes_20220315.csv"
ktaxmap = "${params.kraken2db}ktax_map.k2"
ardb = "${baseDir}/assets/databases/ResGANNCBI_20220915_srst2.fasta"
gamdbpf = "${baseDir}/assets/databases/PF-Replicons_20220916.fasta"
hvgamdb = "${baseDir}/assets/databases/HyperVirulence_20220414.fasta"
//busco db prep
busco_config = "${baseDir}/conf/modules.config"
publish_dir_mode = 'copy'
// References
genome = 'R64-1-1'
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
// MultiQC options
multiqc_config = null
multiqc_title = null
max_multiqc_email_size = '25.MB'
// Boilerplate options
tracedir = "${params.outdir}/pipeline_info"
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'new_samplesheet,results,placeholder,zipped_sketch,terra,fasta,genomes,genome,igenomes_ignore,igenomes_base,minlength,phred,ardb,hvgamdb,gamdbpf,taxa,ncbi_assembly_stats,refseq_fasta_database,bbdukdb,path2db,ktaxmap,busco_config'
enable_conda = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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")
}
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
}
cdcsge { includeConfig "conf/cdcsge.config" }
terra { includeConfig 'conf/terra.config' }
hpc_custom { includeConfig 'conf/HPC_Template.config' }
test { includeConfig 'conf/test.config' }
test_pass { includeConfig 'conf/test_pass.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
// 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_${trace_timestamp}.svg"
}
manifest {
name = 'cdcgov/phoenix'
author = 'Maria Diaz, Nicholas Vlachos, Rich Stanton, Alyssa Kent and Jill Hagey'
homePage = 'https://github.com/CDCgov/phoenix'
description = '🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
version = '1.0.0'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}