Nextflow Registry | nf-core/traitar/run@0.0.0-e2d3f0d

nf-core/traitar/run @ 0.0.0-e2d3f0d

Traitar3 - predict microbial phenotypes from genomic sequences using protein families

Latest version: 0.0.0-e2d3f0d

Total downloads: 2

Source: nf-core/modules

Authors: @brovolia

Maintainers: @brovolia

Traitar3 - predict microbial phenotypes from genomic sequences using protein families

Add the following snippet to your workflow script to include this module.

include { TRAITAR } from 'nf-core/traitar/run'

MIT License

Process

`Name`	`TRAITAR`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`fasta` file	Input sequences in FASTA format (nucleotides, genes, or annotation summary), can be gzipped `*.{fa,fasta,faa,fna,fa.gz,fasta.gz,faa.gz,fna.gz}`

`input_type` string	Input type specifying the format of input sequences (from_nucleotides, from_genes, or from_annotation_summary)

`pfam_db` directory	PFAM database directory created by traitar/pfamget module or downloaded from https://ftp.ebi.ac.uk/pub/databases/Pfam/ `pfam_data`

Output 7 channels

#1 gene_prediction tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*/gene_prediction/` directory	Gene prediction directory

#2 pfam_annotation tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*/annotation/pfam/` directory	Pfam annotation directory

#3 predictions_raw tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`/predictions_.txt` file	Raw phenotype predictions

#4 predictions_flat tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`/phenotype_prediction/predictions_flat_.txt` file	Flattened phenotype predictions

#5 versions_traitar tuple

`${task.process}` string	The name of the process
`traitar` string	The name of the tool
`traitar --version 2>&1 \| tail -1` eval	The expression to obtain the version of the tool

#6 predictions_combined tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*/phenotype_prediction/predictions_majority-vote_combined.txt` file	Combined phenotype predictions using majority voting

#7 predictions_single_votes tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*/phenotype_prediction/predictions_single-votes_combined.txt` file	Single vote phenotype predictions

Tool	Description	Homepage
traitar	Traitar3 - the microbial trait analyzer (for Python3)	https://github.com/nick-youngblut/traitar3

Version	0.0.0-e2d3f0d
Commit ID	e2d3f0ddf4a74a4a9031f3caea2e9deaec5a440b
Release Date	28 Apr 2026 21:16:01 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ftraitar%2Frun/0.0.0-e2d3f0d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/traitar/run/blobs/sha256:d70861e940ca648458a997efd9e4763c49824500e5b0e87fb0f143f888a6296e
Size	4.1 KB