Nextflow Registry | nf-core/clustalo/align@0.0.0-6c4ed3a

nf-core/clustalo/align @ 0.0.0-6c4ed3a

Align sequences using Clustal Omega

alignment MSA genomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:09:24 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fclustalo%2Falign/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/clustalo/align/blobs/sha256:5e2ec06d41f233474e22574d38230efe64dfd80ad4881e336a7d7b3d01ededbc
Size	3.6 KB
Checksum	sha256:5e2ec06d41f233474e22574d38230efe64dfd80ad4881e336a7d7b3d01ededbc
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a