Nextflow Registry | nf-core/tcoffee/consensus@0.0.0-0c7146d

nf-core/tcoffee/consensus @ 0.0.0-0c7146d

Computes a consensus alignment using T_COFFEE

alignment MSA genomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @luisas

Maintainers: @luisas

Computes a consensus alignment using T_COFFEE

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

include { TCOFFEE_CONSENSUS } from 'nf-core/tcoffee/consensus'

MIT License

Process

`Name`	`TCOFFEE_CONSENSUS`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`aln` file	List of multiple sequence alignments in FASTA format to be used to compute the consensus `*.{fa,fasta}`

#2 tuple

`meta2` map	Groovy Map containing tree information e.g. `[ id:'test_tree']`
`tree` file	Input guide tree in Newick format `*.{dnd}`

`compress` boolean	Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded.

Output 4 channels

#1 eval tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]` `*.{fa,fasta,aln}`
`*.{score_html,sp_ascii}` file	Consensus evaluation file. `*.{score_html, score_ascii}`

#2 alignment tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]` `*.{fa,fasta,aln}`
`*.{aln,aln.gz}` file	Alignment file in FASTA format. May be gzipped. `*.aln{.gz,}`

#3 versions_pigz tuple

`${task.process}` string	The name of the process
`pigz` string	The name of the tool
`pigz --version 2>&1 \| sed "s/^.pigz[[:space:]]//"` eval	The expression to obtain the version of the tool

#4 versions_tcoffee tuple

`${task.process}` string	The name of the process
`tcoffee` string	The name of the tool
`t_coffee -version \| awk '{gsub("Version_", ""); print \$3}'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
tcoffee	A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.	http://www.tcoffee.org/Projects/tcoffee/
pigz	Parallel implementation of the gzip algorithm.	https://zlib.net/pigz/

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:43:13 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Ftcoffee%2Fconsensus/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/tcoffee/consensus/blobs/sha256:485b9bb5a969afb5cc32cc6b7ec7e381a71d4eecd13ee7b0da30fcc7c3433e4a
Size	3.5 KB
Checksum	sha256:485b9bb5a969afb5cc32cc6b7ec7e381a71d4eecd13ee7b0da30fcc7c3433e4a
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:49:29 (UTC)		3	3.5 KB
0.0.0-0c7146d	08 Apr 2026 19:43:13 (UTC)		3	3.5 KB