traitar_download

Tags: phenotype traits pfam database download run-scope

Download the Pfam database required by Traitar.

Fetches the pre-compiled Pfam database required by Traitar for microbial phenotype prediction. The database contains Pfam HMM models used for protein family annotation during trait prediction.

Internet & Storage Required

This process requires an active internet connection and significant disk space to store the Pfam database files (~1.2GB).

Outputs

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

Field	Type	Description
db	Path	The Pfam-A HMM file for Traitar
logs	Set<Path?>	Optional program specific log files

Parameters

Traitar Download Parameters

Parameter	Type	Default	Description
--traitar_db	string	-	Path a Traitar database (should contain the Pfam-A.hmm file)
--download_traitar	boolean	false	Download the Pfam database to the path given by --traitar_db

Used By

Subworkflows

• traitar - Predict phenotypic traits from microbial genomes

Workflows

• traitar - Predict phenotypic traits from microbial genomes

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)

• Traitar
  Weimann A, Mooren K, Frank J, Pope PB, Gronow S, So AP From genomes to phenotypes: Traitar, the microbial trait analyzer. mSystems 1(6), e00101-16 (2016)

Source

View source on GitHub

Version

TRAITAR_DOWNLOAD:
    - traitar: 3.0.1