traitar_run

Tags: phenotype traits pfam sample-scope

Predict phenotypic traits from microbial genomes.

Uses Traitar to predict phenotypic traits from nucleotide sequences. Traitar annotates protein families using Pfam and applies machine learning models to predict 67 diverse microbial traits.

Database Required

Requires a Pfam database directory (downloaded via traitar pfam or the download module).

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

db: Path

Name	Type	Description
db	Path	Pfam-A HMM file for Traitar

Outputs

record (
    meta: Record,
    majority_tsv: Path,
    single_tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
majority_tsv	Path	Majority-vote combined phenotype trait predictions
single_tsv	Path	Single-votes combined phenotype trait predictions
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

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_RUN:
    - traitar: 3.0.1