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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uphl-biongs/walkercreek 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
platform = null
fasta = 'https://ftp.ncbi.nih.gov/genomes/INFLUENZA/influenza.fna.gz'
// Reference data
irma_flu_reference = "${projectDir}/ref/irma_flu.fasta"
irma_flu_index = "${projectDir}/ref/irma_flu.fasta.fai"
irma_flu_gff = "${projectDir}/ref/irma_flu.gff"
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
h1n1_freyja_ref_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/H1N1/latest/reference.fasta'
h1n1_freyja_barcodes_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/H1N1/latest/barcode.csv'
h1n1_freyja_barcode_html_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/H1N1/latest/barcode.html'
h1n1_freyja_auspice_tree_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/H1N1/latest/auspice_tree.json'
h3n2_freyja_ref_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/H3N2/latest/reference.fasta'
h3n2_freyja_barcodes_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/H3N2/latest/barcode.csv'
h3n2_freyja_barcode_html_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/H3N2/latest/barcode.html'
h3n2_freyja_auspice_tree_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/H3N2/latest/auspice_tree.json'
h5nx_freyja_ref_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/H5Nx/latest/reference.fasta'
h5nx_freyja_barcodes_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/H5Nx/latest/barcode.csv'
h5nx_freyja_barcode_html_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/H5Nx/latest/barcode.html'
h5nx_freyja_auspice_tree_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/H5Nx/latest/auspice_tree.json'
b_vic_freyja_ref_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/FLU-B-VIC/latest/reference.fasta'
b_vic_freyja_barcodes_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/FLU-B-VIC/latest/barcode.csv'
b_vic_freyja_barcode_html_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/FLU-B-VIC/latest/barcode.html'
b_vic_freyja_auspice_tree_url = 'https://raw.githubusercontent.com/andersen-lab/Freyja-barcodes/main/FLU-B-VIC/latest/auspice_tree.json'
h1n1_freyja_ref = "${projectDir}/ref/h1n1_reference.fasta"
h1n1_freyja_barcodes = "${projectDir}/ref/h1n1_barcode.csv"
h1n1_freyja_barcode_html = "${projectDir}/ref/h1n1_barcode.html"
h1n1_freyja_auspice_tree = "${projectDir}/ref/h1n1_auspice_tree.json"
h3n2_freyja_ref = "${projectDir}/ref/h3n2_reference.fasta"
h3n2_freyja_barcodes = "${projectDir}/ref/h3n2_barcode.csv"
h3n2_freyja_barcode_html = "${projectDir}/ref/h3n2_barcode.html"
h3n2_freyja_auspice_tree = "${projectDir}/ref/h3n2_auspice_tree.json"
h5nx_freyja_ref = "${projectDir}/ref/h5nx_reference.fasta"
h5nx_freyja_barcodes = "${projectDir}/ref/h5nx_barcode.csv"
h5nx_freyja_barcode_html = "${projectDir}/ref/h5nx_barcode.html"
h5nx_freyja_auspice_tree = "${projectDir}/ref/h5nx_auspice_tree.json"
b_vic_freyja_ref = "${projectDir}/ref/b_vic_reference.fasta"
b_vic_freyja_barcodes = "${projectDir}/ref/b_vic_barcode.csv"
b_vic_freyja_barcode_html = "${projectDir}/ref/b_vic_barcode.html"
b_vic_freyja_auspice_tree = "${projectDir}/ref/b_vic_auspice_tree.json"
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = './results'
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
validate_params = true
show_hidden_params = false
schema_ignore_params = "genomes"
enable_conda = false
// FastQC options
adapter_fasta = "${projectDir}/assets/adapter.fasta"
save_trimmed_fail = false
save_merged = false
trim_len = 50
skip_fastqc = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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'
// walkercreek options
save_debug = false
irma_module = ''
genome_length = 13500
keep_ref_deletions = true
skip_ncbi_sra_human_scrubber = false
skip_vadr = false
skip_kraken2 = false
skip_nextclade = false
skip_snpeff = false
adapters_fasta = 'https://raw.githubusercontent.com/BioInfoTools/BBMap/master/resources/adapters.fa'
iims_primers_fasta = "${projectDir}/assets/iiMS_primers.fasta"
illumina_primers_fasta = "${projectDir}/assets/illumina_primers.fasta"
project_db_dir = "${projectDir}/data"
project_db_dir_ww = "${projectDir}/data_ww"
phix_fasta = 'https://github.com/BioInfoTools/BBMap/raw/master/resources/phix174_ill.ref.fa.gz'
kraken_db_dir = "${projectDir}/data/kraken_db"
flukraken_db_dir = "${projectDir}/data_ww/flukraken2"
flukrakendb_file = "${projectDir}/ref/flukraken2.tar.gz"
krakendb = 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20230314.tar.gz'
flukrakendb = 'https://github.com/jhuapl-bio/mytax/raw/refs/heads/master/databases/flukraken2.tar.gz'
nextclade_dataset = null
cacheDir = '.nextflow/cache'
min_sample_reads = 100
longread_adaptertrimming_tool = "porechop_abi"
skip_adapter_trimming = false
save_porechop_reads = false
save_filtlong_reads = false
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load uphl-biongs/walkercreek custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/walkercreek.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/walkercreek profiles: ${params.custom_config_base}/pipeline/walkercreek.config")
// }
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
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
}
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
}
test { includeConfig 'conf/test.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}.html"
}
manifest {
name = 'UPHL-BioNGS/walkercreek'
author = """Tom Iverson"""
homePage = 'https://github.com/UPHL-BioNGS/walkercreek'
description = """A nextflow pipeline for influenza genomic analysis"""
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=24.04.2'
version = '3.0'
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
}
}
}