defensefinder_update

Tags: bacteria defense database download hmm casfinder crispr run-scope

Download and package the DefenseFinder and CasFinder model databases.

Fetches the latest HMM profiles from the DefenseFinder and CasFinder repositories, then packages them into a single tarball for use by the DefenseFinder module.

Internet Required

This process requires an active internet connection to fetch the models from GitHub.

Outputs

record (
    db: Path,
    logs: Set<Path?>
)

Field	Type	Description
db	Path	A compressed tarball containing both DefenseFinder and CasFinder models
logs	Set<Path?>	Optional program specific log files

Parameters

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_UPDATE:
    - defense-finder: 2.0.1