Nextflow Registry | nf-core/gubbins@0.0.0-0c7146d

nf-core/gubbins @ 0.0.0-0c7146d

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.

recombination alignment phylogeny

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @avantonder

Maintainers: @avantonder

Summary

Get started

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

include { GUBBINS } from 'nf-core/gubbins'

License

MIT License

Process

`Name`	`GUBBINS`

Input 1 channel

`alignment` file	fasta alignment file `*.{fasta,fas,fa,aln}`

Output 10 channels

#1 gff

`*.gff` file	Recombination predictions in gff format `*.{gff}`

#2 vcf

`*.vcf` file	SNP distribution `*.{vcf}`

#3 tree

`*.final_tree.tre` file	Recombination removed RAxML phylogenetic tree `*.{final_tree.tre}`

#4 fasta

`*.fasta` file	Filtered variant alignment in fasta format `*.{fasta}`

#5 stats

`*.csv` file	Per branch statistics `*.{csv}`

#6 phylip

`*.phylip` file	Filtered variant alignment in phylip format `*.{phylip}`

#7 embl_branch

`*.branch_base_reconstruction.embl` file	Branch base reconstruction `*.{branch_base_reconstruction.embl}`

#8 tree_labelled

`*.node_labelled.final_tree.tre` file	Recombination removed RAxML phylogenetic tree (nodes labelled) `*.{node_labelled.final_tree.tre}`

#9 embl_predicted

`*.recombination_predictions.embl` file	Recombination predictions in embl format `*.{recombination_predictions.embl}`

#10 versions_gubbins tuple

`${task.process}` string	The name of the process
`gubbins` string	The name of the tool
`run_gubbins.py --version 2>&1` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
gubbins	Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.	https://sanger-pathogens.github.io/gubbins/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:45:50 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgubbins/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gubbins/blobs/sha256:9fdfcf1e1ad9353e594f6b87408382b999efded8358489713b7dfd679376c5bc
Size	3.0 KB
Checksum	sha256:9fdfcf1e1ad9353e594f6b87408382b999efded8358489713b7dfd679376c5bc
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:45:50 (UTC)		1	3.0 KB	-