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nextflow.config
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nextflow.config
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/*
========================================================================================
nf-core/viralrecon Nextflow config file
========================================================================================
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
platform = null
protocol = null
// Reference genome options
genome = null
primer_set = null
primer_set_version = null
primer_fasta = null
primer_left_suffix = '_LEFT'
primer_right_suffix = '_RIGHT'
save_reference = false
// Nanopore options
fastq_dir = null
fast5_dir = null
sequencing_summary = null
min_barcode_reads = 100
min_guppyplex_reads = 10
artic_minion_caller = 'nanopolish'
artic_minion_aligner = 'minimap2'
artic_minion_medaka_model = null
skip_pycoqc = false
skip_nanoplot = false
// Nanopore/Illumina options
asciigenome_read_depth = 50
asciigenome_window_size = 50
multiqc_title = null
multiqc_config = null
max_multiqc_email_size = '25.MB'
skip_mosdepth = false
skip_pangolin = false
skip_nextclade = false
skip_asciigenome = false
skip_variants_quast = false
skip_multiqc = false
// Illumina QC, read trimming and filtering options
kraken2_db = 's3://nf-core-awsmegatests/viralrecon/input_data/kraken2_human.tar.gz'
kraken2_db_name = 'human'
kraken2_variants_host_filter = false
kraken2_assembly_host_filter = true
save_trimmed_fail = false
skip_fastqc = false
skip_kraken2 = false
skip_fastp = false
skip_cutadapt = false
// Illumina variant calling options
callers = null
min_mapped_reads = 1000
ivar_trim_noprimer = false
ivar_trim_offset = null
filter_duplicates = false
save_unaligned = false
save_mpileup = false
skip_ivar_trim = false
skip_markduplicates = true
skip_picard_metrics = false
skip_snpeff = false
skip_consensus = false
skip_variants = false
// Illumina de novo assembly options
assemblers = 'spades'
spades_mode = 'rnaviral'
spades_hmm = null
blast_db = null
skip_bandage = false
skip_blast = false
skip_abacas = false
skip_plasmidid = false
skip_assembly_quast = false
skip_assembly = false
// Boilerplate options
outdir = './results'
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
enable_conda = false
singularity_pull_docker_container = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,modules,igenomes_base'
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = [:]
config_profile_name = null
config_profile_description = null
config_profile_contact = null
config_profile_url = 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 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: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/viralrecon custom config.
// The default 'genomes.config' used by the pipeline can be found here and is auto-loaded via the pipeline config:
// https://github.com/nf-core/configs/blob/master/conf/pipeline/viralrecon/genomes.config
try {
includeConfig "${params.custom_config_base}/pipeline/viralrecon.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/viralrecon profiles: ${params.custom_config_base}/pipeline/viralrecon.config")
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_sispa { includeConfig 'conf/test_sispa.config' }
test_nanopore { includeConfig 'conf/test_nanopore.config' }
test_full { includeConfig 'conf/test_full.config' }
test_full_illumina { includeConfig 'conf/test_full.config' }
test_full_nanopore { includeConfig 'conf/test_full_nanopore.config' }
test_full_sispa { includeConfig 'conf/test_full_sispa.config' }
}
// Increase time available to build Conda environment
conda { createTimeout = "120 min" }
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.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_${trace_timestamp}.svg"
}
manifest {
name = 'nf-core/viralrecon'
author = 'Sarai Varona and Sara Monzon'
homePage = 'https://github.com/nf-core/viralrecon'
description = 'Assembly and intrahost/low-frequency variant calling for viral samples'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.0'
version = '2.2'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}