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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/funcscan Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = 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/'
// To stop the random warning coming from nf-validation, remove on upgrade to nf-schema
monochromeLogs = null
// Taxonomy classification options
run_taxa_classification = false
taxa_classification_tool = 'mmseqs2'
taxa_classification_mmseqs_db = null
taxa_classification_mmseqs_db_id = 'Kalamari'
taxa_classification_mmseqs_db_savetmp = false
taxa_classification_mmseqs_taxonomy_savetmp = false
taxa_classification_mmseqs_taxonomy_searchtype = 2
taxa_classification_mmseqs_taxonomy_lcaranks = 'kingdom,phylum,class,order,family,genus,species'
taxa_classification_mmseqs_taxonomy_taxlineage = 1
taxa_classification_mmseqs_taxonomy_sensitivity = '5.0'
taxa_classification_mmseqs_taxonomy_orffilters = '2.0'
taxa_classification_mmseqs_taxonomy_lcamode = 3
taxa_classification_mmseqs_taxonomy_votemode = 1
// Annotation options
annotation_tool = 'pyrodigal'
save_annotations = false
annotation_prodigal_singlemode = false
annotation_prodigal_closed = false
annotation_prodigal_transtable = 11
annotation_prodigal_forcenonsd = false
annotation_pyrodigal_singlemode = false
annotation_pyrodigal_closed = false
annotation_pyrodigal_transtable = 11
annotation_pyrodigal_forcenonsd = false
annotation_bakta_db = null
annotation_bakta_db_downloadtype = 'full'
annotation_bakta_singlemode = false
annotation_bakta_mincontiglen = 1
annotation_bakta_translationtable = 11
annotation_bakta_gram = '?'
annotation_bakta_complete = false
annotation_bakta_renamecontigheaders = false
annotation_bakta_compliant = false
annotation_bakta_trna = false
annotation_bakta_tmrna = false
annotation_bakta_rrna = false
annotation_bakta_ncrna = false
annotation_bakta_ncrnaregion = false
annotation_bakta_crispr = false
annotation_bakta_skipcds = false
annotation_bakta_pseudo = false
annotation_bakta_skipsorf = false
annotation_bakta_gap = false
annotation_bakta_ori = false
annotation_bakta_activate_plot = false
annotation_prokka_singlemode = false
annotation_prokka_rawproduct = false
annotation_prokka_kingdom = 'Bacteria'
annotation_prokka_gcode = 11
annotation_prokka_cdsrnaolap = false
annotation_prokka_rnammer = false
annotation_prokka_mincontiglen = 1
annotation_prokka_evalue = 0.000001
annotation_prokka_coverage = 80
annotation_prokka_compliant = true
annotation_prokka_addgenes = false
annotation_prokka_retaincontigheaders = false
// Database downloading options
save_db = false
// AMP options
run_amp_screening = false
amp_skip_amplify = false
amp_skip_macrel = false
amp_skip_ampir = false
amp_ampir_model = 'precursor'
amp_ampir_minlength = 10
amp_run_hmmsearch = false
amp_hmmsearch_models = null
amp_hmmsearch_savealignments = false
amp_hmmsearch_savetargets = false
amp_hmmsearch_savedomains = false
amp_ampcombi_db = null
amp_ampcombi_parsetables_cutoff = 0.6
amp_ampcombi_parsetables_ampir = '.ampir.tsv'
amp_ampcombi_parsetables_amplify = '.amplify.tsv'
amp_ampcombi_parsetables_macrel = '.macrel.prediction'
amp_ampcombi_parsetables_hmmsearch = '.hmmer_hmmsearch.txt'
amp_ampcombi_parsetables_aalength = 100
amp_ampcombi_parsetables_dbevalue = 5
amp_ampcombi_parsetables_hmmevalue = 0.06
amp_ampcombi_parsetables_windowstopcodon = 60
amp_ampcombi_parsetables_windowtransport = 11
amp_ampcombi_parsetables_removehitswostopcodons = false
amp_ampcombi_cluster_covmode = 0
amp_ampcombi_cluster_mode = 1
amp_ampcombi_cluster_coverage = 0.8
amp_ampcombi_cluster_seqid = 0.4
amp_ampcombi_cluster_sensitivity = 4.0
amp_ampcombi_cluster_removesingletons = false
amp_ampcombi_cluster_minmembers = 0
// ARG options
run_arg_screening = false
arg_skip_fargene = false
arg_fargene_hmmmodel = 'class_a,class_b_1_2,class_b_3,class_c,class_d_1,class_d_2,qnr,tet_efflux,tet_rpg,tet_enzyme'
arg_fargene_savetmpfiles = false
arg_fargene_minorflength = 90
arg_fargene_score = null
arg_fargene_translationformat = 'pearson'
arg_fargene_orffinder = false
arg_skip_rgi = false
arg_rgi_db = null
arg_rgi_savejson = false
arg_rgi_savetmpfiles = false
arg_rgi_alignmenttool = 'BLAST'
arg_rgi_includeloose = false
arg_rgi_includenudge = false
arg_rgi_lowquality = false
arg_rgi_data = 'NA'
arg_rgi_split_prodigal_jobs = true
arg_skip_amrfinderplus = false
arg_amrfinderplus_db = null
arg_amrfinderplus_identmin = -1
arg_amrfinderplus_coveragemin = 0.5
arg_amrfinderplus_translationtable = 11
arg_amrfinderplus_plus = false
arg_amrfinderplus_name = false
arg_skip_deeparg = false
arg_deeparg_db = null
arg_deeparg_db_version = 2 // Make sure to update on module version bump!
arg_deeparg_model = 'LS'
arg_deeparg_minprob = 0.8
arg_deeparg_alignmentidentity = 50
arg_deeparg_alignmentevalue = 1e-10
arg_deeparg_alignmentoverlap = 0.8
arg_deeparg_numalignmentsperentry = 1000
arg_skip_abricate = false
arg_abricate_db_id = 'ncbi'
arg_abricate_db = null
arg_abricate_minid = 80
arg_abricate_mincov = 80
arg_hamronization_summarizeformat = 'tsv'
// BGC options
run_bgc_screening = false
bgc_mincontiglength = 3000
bgc_savefilteredcontigs = false
bgc_skip_antismash = false
bgc_antismash_db = null
bgc_antismash_installdir = null
bgc_antismash_cbgeneral = false
bgc_antismash_cbknownclusters = false
bgc_antismash_cbsubclusters = false
bgc_antismash_smcogtrees = false
bgc_antismash_ccmibig = false
bgc_antismash_contigminlength = 3000
bgc_antismash_hmmdetectionstrictness = 'relaxed'
bgc_antismash_taxon = 'bacteria'
bgc_skip_deepbgc = false
bgc_deepbgc_db = null
bgc_deepbgc_score = 0.5
bgc_deepbgc_prodigalsinglemode = false
bgc_deepbgc_mergemaxproteingap = 0
bgc_deepbgc_mergemaxnuclgap = 0
bgc_deepbgc_minnucl = 1
bgc_deepbgc_minproteins = 1
bgc_deepbgc_mindomains = 1
bgc_deepbgc_minbiodomains = 0
bgc_deepbgc_classifierscore = 0.5
bgc_skip_gecco = false
bgc_gecco_cds = 3
bgc_gecco_threshold = 0.8
bgc_gecco_pfilter = 0.000000001
bgc_gecco_edgedistance = 0
bgc_gecco_mask = false
bgc_run_hmmsearch = false
bgc_hmmsearch_models = null
bgc_hmmsearch_savealignments = false
bgc_hmmsearch_savetargets = false
bgc_hmmsearch_savedomains = 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/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes,igenomes_base,fasta,monochromeLogs'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/funcscan custom profiles from different institutions.
try {
includeConfig "${params.custom_config_base}/pipeline/funcscan.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/funcscan profiles: ${params.custom_config_base}/pipeline/funcscan.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_bakta { includeConfig 'conf/test_bakta.config' }
test_prokka { includeConfig 'conf/test_prokka.config' }
test_bgc_bakta { includeConfig 'conf/test_bgc_bakta.config' }
test_bgc_prokka { includeConfig 'conf/test_bgc_prokka.config' }
test_bgc_pyrodigal { includeConfig 'conf/test_bgc_pyrodigal.config' }
test_taxonomy_bakta { includeConfig 'conf/test_taxonomy_bakta.config' }
test_taxonomy_prokka { includeConfig 'conf/test_taxonomy_prokka.config' }
test_taxonomy_pyrodigal { includeConfig 'conf/test_taxonomy_pyrodigal.config' }
test_full { includeConfig 'conf/test_full.config' }
test_nothing { includeConfig 'conf/test_nothing.config' }
test_preannotated { includeConfig 'conf/test_preannotated.config' }
test_preannotated_bgc { includeConfig 'conf/test_preannotated_bgc.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 'nf-validation@1.1.3' // 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/funcscan'
author = """Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates"""
homePage = 'https://github.com/nf-core/funcscan'
description = """Pipeline for screening for functional components of assembled contigs"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.2.0dev'
doi = '10.5281/zenodo.7643099'
}
// 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
}
}
}