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

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

Aligns protein structures using UPP

alignment MSA genomics structure

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @luisas

Maintainers: @luisas

Aligns protein structures using UPP

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

include { UPP_ALIGN } from 'nf-core/upp/align'

MIT License

Process

`Name`	`UPP_ALIGN`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test']`
`fasta_unaligned` file	Unaligned sequence file. If no backbone tree nor alignment is given, the sequence file will be randomly split into a backbone set and query set `*.{fa,fna,faa,fasta}`
`fasta_aligned` file	Aligned sequence file. (optional) `*.{fa,fna,faa,fasta,aln}`

#2 tuple

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

`compress` boolean	Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression.

Output 2 channels

#1 alignment tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test']`
`*.aln{.gz,}` file	Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false `*.aln{.gz,}`

#2 versions_sepp tuple

`${task.process}` string	The name of the process
`sepp` string	The name of the tool
`run_upp.py -v \| grep "run_upp" \| cut -f2 -d" "` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
upp	SATe-enabled phylogenetic placement	https://github.com/smirarab/sepp/tree/master

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:21:04 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fupp%2Falign/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/upp/align/blobs/sha256:d3cc7cb8de4fe9da4b028cd062081d1acfbdc9067da749da34a28de6a6e3e156
Size	3.1 KB
Checksum	sha256:d3cc7cb8de4fe9da4b028cd062081d1acfbdc9067da749da34a28de6a6e3e156
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:21:04 (UTC)		1	3.1 KB	-