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

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

Align sequences using Clustal Omega

alignment MSA genomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @luisas @joseespinosa

Maintainers: @luisas @joseespinosa @lrauschning

Align sequences using Clustal Omega

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

include { CLUSTALO_ALIGN } from 'nf-core/clustalo/align'

MIT License

Process

`Name`	`CLUSTALO_ALIGN`

Input 7 channels

#1 tuple

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

#2 tuple

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

`hmm_in` file	HMM file for profile alignment `*.hmm`

`hmm_batch` file	specify HMMs for individual sequences `*.hmm`

`profile1` file	Pre-aligned multiple sequence file 1 `*.{alnfaa,faa,fa,fasta}`

`profile2` file	Pre-aligned multiple sequence file 2 `*.{alnfaa,faa,fa,fasta}`

`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 3 channels

#1 alignment tuple

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

#2 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

#3 versions_clustalo tuple

`${task.process}` string	The name of the process
`clustalo` string	The name of the tool
`clustalo --version` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
clustalo	Latest version of Clustal: a multiple sequence alignment program for DNA or proteins	http://www.clustal.org/omega/
pigz	Parallel implementation of the gzip algorithm.	https://zlib.net/pigz/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:31:01 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fclustalo%2Falign/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/clustalo/align/blobs/sha256:716314b3605fce09171ce57d56cb88917e1ff89b4e14df05e4027d0b4c1a4f0b
Size	3.6 KB
Checksum	sha256:716314b3605fce09171ce57d56cb88917e1ff89b4e14df05e4027d0b4c1a4f0b
Downloads	1

Version	Date	Status	Downloads	Size	Diff