defensefinder_run

Tags: bacteria defense-systems antiviral phage crispr restriction-modification hmm macsyfinder sample-scope

Detect anti-phage defense systems using HMM profiles.

Uses DefenseFinder to systematically search protein sequences for known antiviral defense systems (e.g., CRISPR-Cas, Restriction-Modification, TA systems, CBASS) using MacSyFinder and a dedicated database of HMM models.

Database Required

Requires the DefenseFinder HMM database to be available.

Inputs

record (
    meta: Record,
    faa: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
faa	Path	Protein sequences in FASTA format (amino acids)

db: Path

Name	Type	Description
db	Path	Directory containing the DefenseFinder models database

Outputs

record (
    meta: Record,
    genes_tsv: Path,
    hmmer_tsv: Path,
    systems_tsv: Path,
    proteins: Path?,
    proteins_index: Path?,
    macsydata_raw: Path?,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
genes_tsv	Path	Tab-delimited list of detected defense genes
hmmer_tsv	Path	Tab-delimited list of HMMER hits used for detection
systems_tsv	Path	Tab-delimited summary of detected defense systems
proteins	Path?	Protein sequences of the detected defense genes
proteins_index	Path?	Index file for the protein sequences
macsydata_raw	Path?	Compressed tarball of raw MacSyFinder data
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

defense-finder Parameters

Parameter	Type	Default	Description
--defensefinder_coverage	number	0.4	Minimal percentage of coverage for each profiles
--defensefinder_dbtype	string	ordered_replicon	The macsyfinder --db-type option (choices: ordered_replicon, gembase, unordered)

Used By

Subworkflows

• defensefinder - Systematically search for anti-phage defense systems.

Workflows

• defensefinder - Systematic identification of anti-phage defense systems.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• DefenseFinder
  Tesson F, Hervé A, Mordret E, Touchon M, d'Humières C, Cury J, Bernheim A Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nature Communications, 13(1), 2561. (2022)

Source

View source on GitHub

Version

DEFENSEFINDER_RUN:
    - defense-finder: 2.0.1