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nextflow.config
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nextflow.config
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/*
* -------------------------------------------------
* CFIA-NCFAD/nf-flu Nextflow config file
* -------------------------------------------------
* Default config options for all environments.
* Cluster-specific config options should be saved
* in the conf folder and imported under a profile
* name here.
*/
params {
// input/output params
input = ''
platform = 'illumina'
outdir = 'results'
ref_db = ''
// IRMA options
irma_module = ''
keep_ref_deletions = true
skip_irma_subtyping_report = true
// H/N subtyping options
pident_threshold = 0.85
min_aln_length = 700
max_top_blastn = 3
// reference data
ncbi_influenza_fasta = 'https://api.figshare.com/v2/file/download/41415330'
ncbi_influenza_metadata = 'https://api.figshare.com/v2/file/download/41415333'
// Slurm scheduler options
slurm_queue = ''
slurm_queue_size = 100
// Boilerplate options
tracedir = "${params.outdir}/pipeline_info"
// Nanopore options
min_sample_reads = 100
variant_caller = 'clair3'
//Medaka Variant calling parameter
medaka_variant_model = 'r941_prom_hac_variant_g507'
medaka_snp_model = 'r941_prom_hac_snp_g507'
//Clair3 Variant calling parameter
clair3_variant_model = 'r941_prom_sup_g5014'
clair3_user_variant_model = ''
// Nanopore/Illumina options
skip_mosdepth = false
output_unmapped_reads = false
// variant filtering parameters
minor_allele_fraction = 0.25
major_allele_fraction = 0.75
// consensus sequence parameters
low_coverage = 10
// VADR parameters
vadr_model_targz = 'https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/flu/1.6.3-2/vadr-models-flu-1.6.3-2.tar.gz'
publish_dir_mode = 'copy'
validate_params = true
help = false
monochrome_logs = false
singularity_pull_docker_container = false
show_hidden_params = false
schema_ignore_params = 'modules,genomes'
}
includeConfig 'conf/base.config'
profiles {
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
// Increase time available to build Conda environment
conda.createTimeout = "120 min"
conda.useMamba = params.use_mamba
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
// Increase time available to build Conda environment
conda.createTimeout = "120 min"
}
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
slurm {
includeConfig 'conf/slurm.config'
}
test_illumina { includeConfig 'conf/test_illumina.config' }
test_nanopore { includeConfig 'conf/test_nanopore.config' }
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${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_${trace_timestamp}.svg"
}
manifest {
name = 'CFIA-NCFAD/nf-flu'
description = 'Influenza A virus genome assembly pipeline'
homePage = 'https://github.com/CFIA-NCFAD/nf-flu'
author = 'Peter Kruczkiewicz, Hai Nguyen'
version = '3.5.3'
nextflowVersion = '!>=22.10.1'
mainScript = 'main.nf'
doi = '10.5281/zenodo.13892044'
}
// Following function from https://github.com/nf-core/vipr/blob/master/nextflow.config#L88
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if(type == 'memory'){
try {
if(obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}