traitar
Tags: phenotype traits pfam sample-scope
Predict phenotypic traits from microbial genomes
This subworkflow uses Traitar to predict phenotypic traits from microbial genomes. It can download and prepare the Pfam database on-demand or use a pre-existing database. It processes each sample individually and aggregates the results into a single consolidated report.
Take
fna: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
fna | Assembled contigs in FASTA format |
database: Path?
download_traitar: Boolean
| Name | Type | Description |
|---|---|---|
database | Path? | Optional pre-existing Pfam-A HMM file |
download_traitar | Boolean | Boolean flag to trigger automatic database download |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
majority_tsv | Majority-vote combined phenotype trait predictions |
single_tsv | Single-votes combined phenotype trait predictions |
run_outputs
| Output | Description |
|---|---|
csv | Merged TSV files with traitar majority-vote and single-vote results from all samples |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- traitar_download - Download the Pfam database required by Traitar.
- traitar_run - Predict phenotypic traits from microbial genomes.
Used By
This subworkflow is used by the following 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)