Nextflow Registry | nf-core/muscle5/super5@0.0.0-0c7146d

nf-core/muscle5/super5 @ 0.0.0-0c7146d

Muscle is a program for creating multiple alignments of amino acid or nucleotide sequences. This particular module uses the super5 algorithm for very big alignments. It can permutate the guide tree according to a set of flags.

align msa multiple sequence alignment

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @alessiovignoli @JoseEspinosa

Maintainers: @alessiovignoli @JoseEspinosa @lrauschning

Summary

Get started

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

include { MUSCLE5_SUPER5 } from 'nf-core/muscle5/super5'

License

MIT License

Process

`Name`	`MUSCLE5_SUPER5`

Input 2 channels

#1 tuple

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

`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', single_end:false ]`
`*.aln{.gz,}` file	Multiple sequence alignment produced in gzipped FASTA format. If '-perm all' is passed in ext.args, this will be multiple files per input! `*.{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_muscle tuple

`${task.process}` string	The name of the process
`muscle` string	The name of the tool
`muscle -version \| head -n 1 \| cut -d " " -f 2 \| sed "s/.linux64//"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
muscle -super5	Muscle v5 is a major re-write of MUSCLE based on new algorithms.	https://drive5.com/muscle5/
pigz	Parallel implementation of the gzip algorithm.	https://zlib.net/pigz/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:58:06 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmuscle5%2Fsuper5/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/muscle5/super5/blobs/sha256:3231df75dbb080ab0a5109800ddd4c43781b33626d71cc9cddd3462f3fd71066
Size	3.2 KB
Checksum	sha256:3231df75dbb080ab0a5109800ddd4c43781b33626d71cc9cddd3462f3fd71066
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:58:06 (UTC)		1	3.2 KB	-