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

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

Aligns sequences using T_COFFEE

alignment MSA genomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @luisas @JoseEspinosa @alessiovignoli

Maintainers: @luisas @JoseEspinosa @lrauschning @alessiovignoli

Aligns sequences using T_COFFEE

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

include { TCOFFEE_ALIGN } from 'nf-core/tcoffee/align'

MIT License

Process

`Name`	`TCOFFEE_ALIGN`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test']`
`fasta` file	Input sequences in FASTA format `*.{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}`

#3 tuple

`meta3` map	Groovy Map containing tree information e.g. `[ id:'test_infos']`
`template` file	T_coffee template file that maps sequences to the accessory information files to be used.
`accessory_information` file	Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures.

`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 lib tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test']`
`.lib` file	optional output, the library generated from the MSA file. `.lib`

#2 alignment tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test']`
`*.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	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:18:57 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ftcoffee%2Falign/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/tcoffee/align/blobs/sha256:0ea016d2c230b18c3a6f3b21d261c10d99497f354aeae565d7857b6b49199f65
Size	3.9 KB