Configuration File
To download a configuration file template users just use --get_config parameter. Using a config file your code is lot more clean and concise.
# get config
nextflow run fmalmeida/bacannot --get_config
# run with config
nextflow run fmalmeida/bacannot -c [path-to-config]
Default configuration
/*
Required / Default Parameters.
This parameters must always be set
*/
params {
/*
DB DOWNLOAD WORKFLOW
*/
// Trigger database download and formatting workflow? --> will not run annotation
// Will download and format a database inside {output} parameter
get_dbs = false
force_update = false
get_zenodo_db = false // download pre-built database
/*
ANNOTATION INPUTS
*/
// Input data mus be given inside a well-formated samplesheet.
// We provide a well-formated example at: https://github.com/fmalmeida/test_datasets/raw/main/bacannot_testing_samplesheets/samplesheet.yaml
//
// Please read the example samplesheet so you can understand how to properly fill it.
//
// It is also documented in the main manual: https://bacannot.readthedocs.io/en/latest/samplesheet
input = null
// Enable reads deduplication for assembly? (If input has reads)
enable_deduplication = false
// path to directory containing databases used by bacannot
// you can download databases with:
// nextflow run fmalmeida/bacannot --get_dbs --output bacannot_dbs -profile <docker/conda/singularity>
bacannot_db = null
/*
GENERAL PARAMETERS
*/
// Main output folder name. More than one bacannot annotation can be redirected
// to the same output parameter. It is good to keep related annotations together.
// A subdirectory with the filename will be created inside this directory.
output = 'results'
// Number of minimum overlapping base pairs required for merging
// Negative values, such as -20, means the number of required overlapping bases for merging.
// Positive values, such as 5, means the maximum distance accepted between features for merging.
// By default (if Blank), this process is not executed. For execution the user needs to provide a value
bedtools_merge_distance = null
/*
* Bakta optional
*/
// If user set path to an existing bakta database, the pipeline will use bakta instead of prokka
bakta_db = null
/*
* Prokka optional parameters
*/
// Include comprehensive PGAP hmm database in prokka annotation instead of TIGRFAM.
// PGAP is big and using it may have higher running times but better results
prokka_use_pgap = false
// Annotation mode: Archaea|Bacteria|Mitochondria|Viruses (default 'Bacteria')
prokka_kingdom = null
// Translation table code. Must be set if the above is set.
// Example: params.prokka_genetic.code = 11
prokka_genetic_code = null
// Use rnammer instead of Barrnap? False or True?
prokka_use_rnammer = false
/*
* Resfinder species panel
*/
// Species panel to be used when annotating with Resfinder.
// It sets a default for all samples in the samplesheet.
// If a sample has a different value inside the samplesheet it will overwrite the value for that sample
// If blank it will not be executed.
// It must be identical (without the *) as written in their webservice https://cge.cbs.dtu.dk/services/ResFinder/.
// E.g. 'Escherichia coli'; 'Klebsiella' ...
resfinder_species = null
/*
* Handling the execution of processes
*
* By default, all processes are executed. These
* parameters tells wheter NOT to run a process.
*
* Which means: false will allow its execution
* while true will create a barrier and skip a process.
*/
// (NOT RUN?) Plasmids annotation (controls PlasmidFinder execution)
skip_plasmid_search = false
// (NOT RUN?) General Virulence annotation (controls VFDB and Victors scan)
skip_virulence_search = false
// (NOT RUN?) Resistance annotation (controls AMRfinder and RGI)
skip_resistance_search = false
// (NOT RUN?) ICE annotation (controls ICEberg annotation)
skip_iceberg_search = false
// (NOT RUN?) prophage annotation (controls PHAST and Phigaro)
skip_prophage_search = false
// (NOT RUN?) KO (KEGG Orthology) annotation
skip_kofamscan = false
// (NOT RUN?) antiSMASH (secondary metabolite) annotation
skip_antismash = false
/*
* Custom databases can be used to annotate additional genes in the genome.
* It runs a BLAST alignment against the genome, therefore, the custom database
* More than one custom database can be given separated by commas.
* Gene headers must be properly formated as described in the
* documentation: https://bacannot.readthedocs.io/en/latest/custom-db
*/
// Custom fastas (PROT / NUCL)
custom_db = null
// Custom annotation using list of NCBI protein accs
ncbi_proteins = null
/*
* Annotation thresholds to be used when scanning specific databases and features
* Select a combination of thresholds that is meaningful for your data. Some of
* the databases are protein-only, others are nucleotide only. We cannnot control
* that and the databases will be scanned either if blastp or blastn using these
* thresholds described here.
*/
// Identity threshold for plasmid annotation
plasmids_minid = 90
// Coverage threshold for plasmid annotation
plasmids_mincov = 60
// Virulence genes identity threshold
blast_virulence_minid = 90
// Virulence genes coverage threshold
blast_virulence_mincov = 90
// AMR genes identity threshold
blast_resistance_minid= 90
// AMR genes coverage threshold
blast_resistance_mincov = 90
// MGEs (ICEs and Phages) identity threshold
blast_MGEs_minid = 85
// MGEs (ICEs and Phages) coverage threshold
blast_MGEs_mincov = 85
// User's custom database identity threshold
blast_custom_minid = 65
// User's custom database coverage threshold
blast_custom_mincov = 65
/*
* Resources allocation configuration
* Defaults only, expecting to be overwritten
*/
// Select versions of bioconda quay.io additional tools
// Tools that are not part of the core of the pipeline,
// but can eventually be used by users
unicycler_version = '0.5.0--py310h6cc9453_3'
flye_version = '2.9--py39h6935b12_1'
bakta_version = '1.7.0--pyhdfd78af_1'
// Max resource options
max_memory = '20.GB'
max_cpus = 16
max_time = '40.h'
}