Nextflow Registry | nf-core/clonalframeml@0.0.0-6c4ed3a

nf-core/clonalframeml @ 0.0.0-6c4ed3a

Predict recomination events in bacterial genomes

fasta multiple sequence alignment recombination

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @rpetit3

Maintainers: @rpetit3

Predict recomination events in bacterial genomes

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

include { CLONALFRAMEML } from 'nf-core/clonalframeml'

MIT License

Process

`Name`	`CLONALFRAMEML`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`newick` file	A Newick formatted tree based on multiple sequence alignment `*.{newick,treefile,dnd}`
`msa` file	A multiple sequence alignment in FASTA format `*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}`

Output 7 channels

#1 em tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.em.txt` file	Point estimates for R/theta, nu, delta and the branch lengths `*.em.txt`

#2 emsim tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.emsim.txt` file	Bootstrapped values for the three parameters R/theta, nu and delta `*.emsim.txt`

#3 fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.ML_sequence.fasta` file	Sequence reconstructed by maximum likelihood `*.ML_sequence.fasta`

#4 newick tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.labelled_tree.newick` file	Tree with all nodes labelled `*.labelled_tree.newick`

#5 status tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.importation_status.txt` file	List of reconstructed recombination events `*.importation_status.txt`

#6 pos_ref tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.position_cross_reference.txt` file	CSV mapping input sequence files to the sequences in the .ML_sequence.fasta `.position_cross_reference.txt`

#7 versions_clonalframeml tuple

`${task.process}` string	The name of the process
`clonalframeml` string	The name of the tool
`ClonalFrameML -version 2>&1 \| sed 's/^.*ClonalFrameML v//'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
clonalframeml	Efficient inferencing of recombination in bacterial genomes	https://github.com/xavierdidelot/ClonalFrameML

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:09:22 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fclonalframeml/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/clonalframeml/blobs/sha256:d3876271c298ddc8284b1ea1ff3d62557a93ad16a1214907d33bbc2a7ea05015
Size	2.8 KB
Checksum	sha256:d3876271c298ddc8284b1ea1ff3d62557a93ad16a1214907d33bbc2a7ea05015