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nextflow.config
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nextflow.config
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/*
========================================================================================
nf-core/mycosnp Nextflow config file
========================================================================================
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
add_sra_file = null
add_vcf_file = null
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
snpeffconfig = "$projectDir/assets/snpeffdb/snpEff.config"
species = 'candida_auris_gca_016772135.1'
genes = 'CAB11_002014'
positions = 'fks1_hs1=221638:221665,fks1_hs2=223782:223805'
exclude = 'synonymous_variant'
// MultiQC options
multiqc_config = null
multiqc_title = null
max_multiqc_email_size = '25.MB'
// Boilerplate options
outdir = './results'
tracedir = "${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 = 'genomes'
enable_conda = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '24.GB'
max_cpus = 4
max_time = '240.h'
// Mycosnp options
save_reference = true
save_alignment = true
sample_ploidy = 1
coverage = 0 // Desired sample coverage used in seqtk_sample, if 0 seqtk_sample will not be preformed.
// rate = 1
gvcfs_filter = 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || DP < 10'
gatkgenotypes_filter = '--min_GQ "50" --keep_GQ_0_refs --min_percent_alt_in_AD "0.8" --min_total_DP "10" --keep_all_ref'
max_amb_samples = 10000000
max_perc_amb_samples = 10
min_depth = 10
publish_dir_mode = 'copy'
rapidnj = true
fasttree = true
//snpeff_build = false
snpeff = false
iqtree = false
raxmlng = false
save_debug = false
mask = true
tmpdir = "$projectDir/tmp"
skip_samples = ""
skip_samples_file = null
skip_combined_analysis = false
skip_phylogeny = false
// Reference files Directory (invalidates specific declarations)
ref_dir = null
// Reference files and indices - all must be provided if one is provided else run will fail.
// Will be ignored if using --ref_dir
ref_masked_fasta = null
ref_fai = null
ref_bwa = null
ref_dict = null
}
env {
TMPDIR = "$params.tmpdir"
_JAVA_OPTIONS= "-Djava.io.tmpdir=$params.tmpdir"
}
// 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 $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
sge { includeConfig 'conf/custom.config' }
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${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_${trace_timestamp}.svg"
}
manifest {
name = 'CDCgov/mycosnp-nf'
author = 'CDC'
homePage = 'https://github.com/CDCgov/mycosnp-nf'
description = 'MycoSNP is a portable workflow for performing whole genome sequencing analysis of fungal organisms, including Candida auris. This method prepares the reference, performs quality control, and calls variants using a reference. MycoSNP generates several output files that are compatible with downstream analytic tools, such as those for used for phylogenetic tree-building and gene variant annotations.'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
version = '1.5'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}