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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
// long read preprocessing options
longread_adaptertrimming_tool = "porechop_abi"
longread_filtering_tool = "filtlong"
// 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
prokka_with_compliance = false
prokka_compliance_centre = null
// 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.gtdb.ecogenomic.org/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_quality = null
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_filtered_longreads = 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'
exclude_unbins_from_postbinning = false
// 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://zenodo.org/records/7401545/files/checkm_data_2015_01_16.tar.gz"
checkm_db = null
save_checkm_data = false
checkm2_db = null
checkm2_db_version = 5571251
// corresponds to Zenodo record ID
save_checkm2_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 // we use --host_genome instead
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
help_full = false
show_hidden = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
trace_report_suffix = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
// 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
// Schema validation default options
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.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']
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
process {
resourceLimits = [
memory: 8.GB,
cpus: 4,
time: 1.h,
]
}
}
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'
}
}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf-core/mag custom profiles from different institutions.
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/mag.config" : "/dev/null"
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / 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'
charliecloud.registry = 'quay.io'
// Load igenomes.config if required
includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
// 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"
}
// Set bash options
process.shell = [
"bash",
"-C", // No clobber - prevent output redirection from overwriting files.
"-e", // Exit if a tool returns a non-zero status/exit code
"-u", // Treat unset variables and parameters as an error
"-o", // Returns the status of the last command to exit..
"pipefail" // ..with a non-zero status or zero if all successfully execute
]
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}
manifest {
name = 'nf-core/mag'
author = """Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry"""
// The author field is deprecated from Nextflow version 24.10.0, use contributors instead
contributors = [
[
name: 'Hadrien Gourlé',
affiliation: 'Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Swden',
email: '',
github: 'HadrienG',
contribution: ['author'],
orcid: '0000-0001-9807-1082 ',
],
[
name: 'Daniel Straub',
affiliation: 'Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany',
email: '',
github: 'd4straub',
contribution: ['author', 'maintainer'],
orcid: '0000-0002-2553-0660 ',
],
[
name: 'Sabrina Krakau',
affiliation: 'Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany',
email: '',
github: 'skrakau',
contribution: ['contributor'],
orcid: '0000-0003-0603-7907 ',
],
[
name: 'Antonia Schuster',
affiliation: 'Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany',
email: '',
github: 'AntoniaSchuster',
contribution: ['author'],
orcid: '',
],
[
name: 'James A. Fellows Yates',
affiliation: 'Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany',
email: '[email protected]',
github: 'jfy133',
contribution: ['maintainer'],
orcid: '0000-0001-5585-6277',
],
[
name: 'Maxime Borry',
affiliation: 'Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany',
email: '',
github: 'maxibor',
contribution: ['contributor'],
orcid: '0000-0001-9140-7559',
],
[
name: 'Jim Downie',
affiliation: 'Wellcome Sanger Institute, Hinxton, UK',
email: '',
github: 'prototaxites',
contribution: ['contributor'],
orcid: '0000-0002-7175-0533',
],
[
name: 'Carson Miller',
affiliation: 'University of Washington, Seattle, USA',
email: '0000-0002-7175-0533',
github: 'CarsonJM',
contribution: ['contributor'],
orcid: '0000-0001-9861-4884',
],
]
homePage = 'https://github.com/nf-core/mag'
description = """Assembly, binning and annotation of metagenomes"""
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=24.04.2'
version = '3.3.1'
doi = '10.1093/nargab/lqac007'
}
// Nextflow plugins
plugins {
id '[email protected]'
}
validation {
defaultIgnoreParams = ["genomes"]
monochromeLogs = params.monochrome_logs
help {
enabled = true
command = "nextflow run nf-core/mag -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
beforeText = """
-\033[2m----------------------------------------------------\033[0m-
\033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m
\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m
\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m
\033[0;32m`._,._,\'\033[0m
\033[0;35m nf-core/mag ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/', '')}" }.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/mag/blob/master/CITATIONS.md
"""
}
summary {
beforeText = validation.help.beforeText
afterText = validation.help.afterText
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'