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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/mag Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
assembly_input = null
single_end = false
// short read preprocessing options
skip_clipping = false
clip_tool = 'fastp'
save_clipped_reads = false
reads_minlength = 15
fastp_save_trimmed_fail = false
fastp_qualified_quality = 15
fastp_cut_mean_quality = 15
adapterremoval_minquality = 2
adapterremoval_adapter1 = 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG'
adapterremoval_adapter2 = 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'
adapterremoval_trim_quality_stretch = false
keep_phix = false
// phix_reference = "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Enterobacteria_phage_phiX174_sensu_lato/all_assembly_versions/GCA_002596845.1_ASM259684v1/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
phix_reference = "${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
save_phixremoved_reads = false
host_fasta = null
host_fasta_bowtie2index = null
host_genome = null
host_removal_verysensitive = false
host_removal_save_ids = false
save_hostremoved_reads = false
bbnorm = false
bbnorm_target = 100
bbnorm_min = 5
save_bbnorm_reads = false
// binning options
bowtie2_mode = null
binning_map_mode = 'group'
save_assembly_mapped_reads = false
skip_binning = false
min_contig_size = 1500
min_length_unbinned_contigs = 1000000
max_unbinned_contigs = 100
skip_prokka = false
// assembly options
coassemble_group = false
spades_options = null
megahit_options = null
skip_spades = false
skip_spadeshybrid = false
skip_megahit = false
skip_quast = false
skip_prodigal = false
// virus identification options
run_virus_identification = false
genomad_db = null
genomad_min_score = 0.7
genomad_splits = 1
// ancient DNA assembly validation options
ancient_dna = false
pydamage_accuracy = 0.5
skip_ancient_damagecorrection = false
freebayes_ploidy = 1
freebayes_min_basequality = 20
freebayes_minallelefreq = 0.33
bcftools_view_high_variant_quality = 30
bcftools_view_medium_variant_quality = 20
bcftools_view_minimal_allelesupport = 3
// taxonomy options
centrifuge_db = null
kraken2_db = null
skip_krona = false
krona_db = null
cat_db = null
cat_db_generate = false
cat_official_taxonomy = false
save_cat_db = false
skip_gtdbtk = false
gtdb_db = "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz"
gtdb_mash = null
gtdbtk_min_completeness = 50.0
gtdbtk_max_contamination = 10.0
gtdbtk_min_perc_aa = 10
gtdbtk_min_af = 0.65
gtdbtk_pplacer_cpus = 1
gtdbtk_pplacer_useram = false
// long read preprocessing options
skip_adapter_trimming = false
keep_lambda = false
longreads_min_length = 1000
longreads_keep_percent = 90
longreads_length_weight = 10
// lambda_reference = "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Escherichia_virus_Lambda/all_assembly_versions/GCA_000840245.1_ViralProj14204/GCA_000840245.1_ViralProj14204_genomic.fna.gz"
lambda_reference = "${baseDir}/assets/data/GCA_000840245.1_ViralProj14204_genomic.fna.gz"
save_lambdaremoved_reads = false
save_porechop_reads = false
save_filtlong_reads = false
// binning options
skip_metabat2 = false
skip_maxbin2 = false
skip_concoct = false
bin_domain_classification = false
bin_domain_classification_tool = 'tiara'
tiara_min_length = 3000
refine_bins_dastool = false
refine_bins_dastool_threshold = 0.5
postbinning_input = 'raw_bins_only'
// Bin QC
skip_binqc = false
binqc_tool = 'busco'
busco_db = null
busco_auto_lineage_prok = false
save_busco_db = false
busco_clean = false
checkm_download_url = "https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz"
checkm_db = null
save_checkm_data = false
run_gunc = false
gunc_database_type = 'progenomes'
gunc_db = null
gunc_save_db = false
// Reproducibility options
megahit_fix_cpu_1 = false
spades_fix_cpus = -1
spadeshybrid_fix_cpus = -1
metabat_rng_seed = 1
// Annotation options
skip_metaeuk = false
metaeuk_mmseqs_db = null
metaeuk_db = null
save_mmseqs_db = false
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
monochromeLogs = null // TODO remove once nf-validation removes the bug
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genome,genomes,igenomes_base,monochromeLogs'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/mag custom profiles from different institutions.
try {
includeConfig "${params.custom_config_base}/pipeline/mag.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/mag profiles: ${params.custom_config_base}/pipeline/mag.config")
}
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.channels = ['conda-forge', 'bioconda', 'defaults']
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
wave {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
wave.enabled = true
wave.freeze = true
wave.strategy = 'conda,container'
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_host_rm { includeConfig 'conf/test_host_rm.config' }
test_hybrid { includeConfig 'conf/test_hybrid.config' }
test_hybrid_host_rm { includeConfig 'conf/test_hybrid_host_rm.config' }
test_busco_auto { includeConfig 'conf/test_busco_auto.config' }
test_ancient_dna { includeConfig 'conf/test_ancient_dna.config' }
test_adapterremoval { includeConfig 'conf/test_adapterremoval.config' }
test_binning_entry { includeConfig 'conf/test_binning_entry.config' }
test_binrefinement { includeConfig 'conf/test_binrefinement.config' }
test_no_clipping { includeConfig 'conf/test_no_clipping.config' }
test_bbnorm { includeConfig 'conf/test_bbnorm.config' }
test_nothing { includeConfig 'conf/test_nothing.config' }
test_virus_identification { includeConfig 'conf/test_virus_identification.config' }
test_single_end { includeConfig 'conf/test_single_end.config' }
test_concoct { includeConfig 'conf/test_concoct.config' }
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
// 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']
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'nf-core/mag'
author = """Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry"""
homePage = 'https://github.com/nf-core/mag'
description = """Assembly, binning and annotation of metagenomes"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '3.1.0'
doi = '10.1093/nargab/lqac007'
}
// 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
}
}
}
// Functions to fix number of cpus to allow reproducibility for MEGAHIT and SPAdes
// if corresponding parameters are specified, number of cpus is not increased with retries
def check_megahit_cpus (x, attempt ) {
if (params.megahit_fix_cpu_1) return 1
else return check_max (x * attempt, 'cpus' )
}
def check_spades_cpus (x, attempt ) {
if (params.spades_fix_cpus != -1) return check_max (params.spades_fix_cpus, 'cpus' )
else return check_max (x * attempt, 'cpus' )
}
def check_spadeshybrid_cpus (x, attempt ) {
if (params.spadeshybrid_fix_cpus != -1) return check_max (params.spadeshybrid_fix_cpus, 'cpus' )
else return check_max (x * attempt, 'cpus' )
}