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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/ampliseq Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
input_fasta = null
input_folder = null
multiregion = null
extension = "/*_R{1,2}_001.fastq.gz"
pacbio = false
iontorrent = false
FW_primer = null
RV_primer = null
classifier = null
metadata = null
// Other options
save_intermediates = false
trunc_qmin = 25
trunc_rmin = 0.75
trunclenf = null
trunclenr = null
max_ee = 2
max_len = null
ignore_failed_filtering = false
min_len = 50
metadata_category = null
metadata_category_barplot = null
double_primer = false
retain_untrimmed = false
cutadapt_min_overlap = 3
cutadapt_max_error_rate = 0.1
exclude_taxa = "mitochondria,chloroplast"
min_frequency = 1
min_samples = 1
multiple_sequencing_runs = false
single_end = false
sample_inference = "independent"
illumina_novaseq = false
illumina_pe_its = false
concatenate_reads = false
cut_its = "none"
its_partial = 0
picrust = false
sbdiexport = false
addsh = false
tax_agglom_min = 2
tax_agglom_max = 6
min_read_counts = 1
ignore_failed_trimming = false
ignore_empty_input_files = false
qiime_adonis_formula = null
seed = 100
filter_ssu = null
min_len_asv = null
max_len_asv = null
filter_codons = null
orf_start = 1
orf_end = null
stop_codons = "TAA,TAG"
pplace_tree = null
pplace_aln = null
pplace_model = null
pplace_alnmethod = 'hmmer'
pplace_taxonomy = null
pplace_name = null
diversity_rarefaction_depth= 500
ancom_sample_min_count = 1
vsearch_cluster = null
vsearch_cluster_id = 0.97
ancom = false
ancombc = false
ancombc_effect_size = 1
ancombc_significance = 0.05
ancombc_formula = null
ancombc_formula_reflvl = null
// Report options
report_template = "${projectDir}/assets/report_template.Rmd"
report_css = "${projectDir}/assets/nf-core_style.css"
report_logo = "${projectDir}/assets/nf-core-ampliseq_logo_light_long.png"
report_title = "Summary of analysis results"
report_abstract = null
// Skipping options
skip_cutadapt = false
skip_dada_quality = false
skip_barrnap = false
skip_qiime = false
skip_qiime_downstream = false
skip_fastqc = false
skip_alpha_rarefaction = false
skip_abundance_tables = false
skip_barplot = false
skip_taxonomy = false
skip_dada_taxonomy = false
skip_dada_addspecies = false
skip_alpha_rarefaction = false
skip_diversity_indices = false
skip_multiqc = false
skip_report = false
// Database options
dada_ref_taxonomy = "silva=138"
dada_assign_taxlevels = null
dada_ref_tax_custom = null
dada_ref_tax_custom_sp = null
cut_dada_ref_taxonomy = false
dada_addspecies_allowmultiple = false
dada_taxonomy_rc = false
sintax_ref_taxonomy = null
qiime_ref_taxonomy = null
qiime_ref_tax_custom = null
kraken2_ref_taxonomy = null
kraken2_assign_taxlevels = null
kraken2_ref_tax_custom = null
kraken2_confidence = 0.0
sidle_ref_taxonomy = null
sidle_ref_tax_custom = null
sidle_ref_tree_custom = null
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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 = 'dada_ref_databases,qiime_ref_databases,sintax_ref_databases,kraken2_ref_databases,sidle_ref_databases,genomes,igenomes_base'
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: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/ampliseq custom profiles from different institutions.
try {
includeConfig "${params.custom_config_base}/pipeline/ampliseq.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/ampliseq profiles: ${params.custom_config_base}/pipeline/ampliseq.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_single { includeConfig 'conf/test_single.config' }
test_multi { includeConfig 'conf/test_multi.config' }
test_doubleprimers { includeConfig 'conf/test_doubleprimers.config' }
test_pacbio_its { includeConfig 'conf/test_pacbio_its.config' }
test_iontorrent { includeConfig 'conf/test_iontorrent.config' }
test_fasta { includeConfig 'conf/test_fasta.config' }
test_failed { includeConfig 'conf/test_failed.config' }
test_full { includeConfig 'conf/test_full.config' }
test_reftaxcustom { includeConfig 'conf/test_reftaxcustom.config' }
test_qiimecustom { includeConfig 'conf/test_qiimecustom.config' }
test_novaseq { includeConfig 'conf/test_novaseq.config' }
test_pplace { includeConfig 'conf/test_pplace.config' }
test_sintax { includeConfig 'conf/test_sintax.config' }
test_its_dada_taxonomy { includeConfig 'conf/test_its_dada_taxonomy.config' }
test_multiregion { includeConfig 'conf/test_multiregion.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
}
// 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/ampliseq'
author = """Daniel Straub, Alexander Peltzer"""
homePage = 'https://github.com/nf-core/ampliseq'
description = """Amplicon sequencing analysis workflow using DADA2 and QIIME2"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '2.11.0'
doi = '10.5281/zenodo.1493841,10.3389/fmicb.2020.550420'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Load ref_databases.config for reference taxonomy
includeConfig 'conf/ref_databases.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
}
}
}