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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/taxprofiler Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
nextflow.enable.strict = true
// Global default params, used in configs
params {
// Input options
input = null
// 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
monochromeLogs = false // required so nf-validation nextflow.enabled.strict works nicely together
hook_url = null
help = false
version = false
// 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 = 'genomes,igenomes_base,fasta,monochromeLogs'
validationShowHiddenParams = false
validate_params = true
// Databases
databases = null
save_untarred_databases = false
// FASTQ preprocessing
skip_preprocessing_qc = false
preprocessing_qc_tool = 'fastqc'
perform_shortread_qc = false
shortread_qc_tool = 'fastp'
shortread_qc_skipadaptertrim = false
shortread_qc_mergepairs = false
shortread_qc_includeunmerged = false
shortread_qc_adapter1 = null
shortread_qc_adapter2 = null
shortread_qc_adapterlist = null
shortread_qc_minlength = 15
shortread_qc_dedup = false
perform_longread_qc = false
longread_qc_skipadaptertrim = false
longread_qc_skipqualityfilter = false
longread_qc_qualityfilter_minlength = 1000
longread_qc_qualityfilter_keeppercent = 90
longread_qc_qualityfilter_targetbases = 500000000
save_preprocessed_reads = false
// Complexity filtering
perform_shortread_complexityfilter = false
shortread_complexityfilter_tool = 'bbduk'
shortread_complexityfilter_entropy = 0.3
shortread_complexityfilter_bbduk_windowsize = 50
shortread_complexityfilter_bbduk_mask = false
shortread_complexityfilter_prinseqplusplus_mode = 'entropy'
shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
shortread_complexityfilter_fastp_threshold = 30
save_complexityfiltered_reads = false
// run merging
perform_runmerging = false
save_runmerged_reads = false
// Host Removal
perform_shortread_hostremoval = false
perform_longread_hostremoval = false
hostremoval_reference = null
shortread_hostremoval_index = null
longread_hostremoval_index = null
save_hostremoval_index = false
save_hostremoval_bam = false
save_hostremoval_unmapped = false
// Publishing final reads going into profiling
save_analysis_ready_fastqs = false
// MALT
run_malt = false
malt_mode = 'BlastN'
malt_generate_megansummary = false
malt_save_reads = false // added via map + database args extension in profiling.nf
// kraken2
run_kraken2 = false
kraken2_save_reads = false // added directly to module in profiling.nf
kraken2_save_readclassifications = false // added directly to module in profiling.nf
kraken2_save_minimizers = false
//krakenuniq
run_krakenuniq = false
krakenuniq_ram_chunk_size = '16G'
krakenuniq_save_reads = false // added directly to module in profiling.nf
krakenuniq_save_readclassifications = false // added directly to module in profiling.nf
krakenuniq_batch_size = 20
// Bracken
run_bracken = false
// centrifuge
run_centrifuge = false
centrifuge_save_reads = false // added directly to module in profiling.nf
// metaphlan
run_metaphlan = false
// kaiju
run_kaiju = false
kaiju_expand_viruses = false
kaiju_taxon_rank = 'species'
// diamond
run_diamond = false
diamond_output_format = 'tsv' // TSV is only format with taxonomic information apparently
diamond_save_reads = false // this will override default diamond output format so no taxonomic profile is generated! added directly to module in profiling.nf
// mOTUs
run_motus = false
motus_use_relative_abundance = false
motus_remove_ncbi_ids = false
motus_save_mgc_read_counts = false
// kmcp
run_kmcp = false
kmcp_mode = 3 // default kmcp profiling value
kmcp_save_search = false
// ganon
run_ganon = false
ganon_report_type = 'reads'
ganon_report_rank = 'default'
ganon_report_toppercentile = 0
ganon_report_mincount = 0
ganon_report_maxcount = 0
ganon_save_readclassifications = false
// krona
run_krona = false
krona_taxonomy_directory = null
// profile standardisation
run_profile_standardisation = false
standardisation_taxpasta_format = 'tsv'
taxpasta_taxonomy_dir = null
taxpasta_add_name = false
taxpasta_add_rank = false
taxpasta_add_lineage = false
taxpasta_add_idlineage = false
taxpasta_add_ranklineage = false
taxpasta_ignore_errors = false
standardisation_motus_generatebiom = 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: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/taxprofiler custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
try {
includeConfig "${params.custom_config_base}/pipeline/taxprofiler.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/taxprofiler profiles: ${params.custom_config_base}/pipeline/taxprofiler.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
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
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
test_nothing { includeConfig 'conf/test_nothing.config' }
test_motus { includeConfig 'conf/test_motus.config' }
test_krakenuniq { includeConfig 'conf/test_krakenuniq.config' }
test_malt { includeConfig 'conf/test_malt.config' }
test_falco { includeConfig 'conf/test_falco.config' }
test_fastp { includeConfig 'conf/test_fastp.config' }
test_adapterremoval { includeConfig 'conf/test_adapterremoval.config' }
test_bbduk { includeConfig 'conf/test_bbduk.config' }
test_prinseqplusplus { includeConfig 'conf/test_prinseqplusplus.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/taxprofiler'
author = """James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, and the nf-core/taxprofiler team"""
homePage = 'https://github.com/nf-core/taxprofiler'
description = """Taxonomic classification and profiling of shotgun short- and long-read metagenomic data"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.1.7dev'
doi = '10.1101/2023.10.20.563221'
}
// 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
}
}
}