Nextflow Registry | nf-core/foldmason/easymsa@0.0.0-0c7146d

nf-core/foldmason/easymsa @ 0.0.0-0c7146d

Aligns protein structures using foldmason

alignment MSA genomics structure

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @luisas

Maintainers: @luisas

Aligns protein structures using foldmason

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

include { FOLDMASON_EASYMSA } from 'nf-core/foldmason/easymsa'

MIT License

Process

`Name`	`FOLDMASON_EASYMSA`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`pdbs` file	Input protein structures in PDB format. `*.{pdb,mmcif}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`tree` file	Input guide tree in Newick format. `*.{dnd,nwk}`

`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 msa_aa tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}_aa.fa${compress ? '.gz' : ''}` file	Fasta file containing the multiple sequence alignment with Amino Acid alphabet `*.{fa}`

#2 msa_3di tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}_3di.fa${compress ? '.gz' : ''}` file	Fasta file containing the multiple sequence alignment with 3Di alphabet `*.{fa}`

#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_foldmason tuple

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

Tool	Description	Homepage
foldmason	Multiple Protein Structure Alignment at Scale with FoldMason	https://github.com/steineggerlab/foldmason

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:01:27 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Ffoldmason%2Feasymsa/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/foldmason/easymsa/blobs/sha256:3972e1fe5bac0453e7bea8af6d0db7583f53c1b83e0258cf2e9be428c89e9002
Size	3.2 KB
Checksum	sha256:3972e1fe5bac0453e7bea8af6d0db7583f53c1b83e0258cf2e9be428c89e9002
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:17:36 (UTC)		3	3.2 KB
0.0.0-0c7146d	08 Apr 2026 19:01:27 (UTC)		4	3.2 KB