Nextflow Registry | nf-core/liftoff@0.0.0-0c7146d

nf-core/liftoff @ 0.0.0-0c7146d

Uses Liftoff to accurately map annotations in GFF or GTF between assemblies of the same, or closely-related species

genome annotation gff3 gtf liftover

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @GallVp

Maintainers: @GallVp

Uses Liftoff to accurately map annotations in GFF or GTF between assemblies of the same, or closely-related species

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

include { LIFTOFF } from 'nf-core/liftoff'

MIT License

Process

`Name`	`LIFTOFF`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`target_fa` file	Target assembly in fasta format (can be gzipped) `*.{fa,fa.gz,fasta,fasta.gz,fas,fas.gz,fsa,fsa.gz}`

`ref_fa` file	Reference assembly in fasta format (can be gzipped) `*.{fa,fa.gz,fasta,fasta.gz,fas,fas.gz,fsa,fsa.gz}`

`ref_annotation` file	Reference assembly annotations in gtf or gff3 format `*.{gtf,gff3}`

`ref_db` file	Name of feature database; if not specified, the -g argument must be provided and a database will be built automatically

Output 4 channels

#1 gff3 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`${prefix}.gff3` file	Lifted annotations for the target assembly in gff3 format `*.gff3`

#2 unmapped_txt tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.unmapped.txt` file	List of unmapped reference annotations `*.unmapped.txt`

#3 polished_gff3 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.polished.gff3` file	Polished lifted annotations for the target assembly in gff3 format `*.polished.gff3`

#4 versions_liftoff tuple

`${task.process}` string	The name of the process
`liftoff` string	The name of the tool
`liftoff --version \| sed "s/v//"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
liftoff	Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species	https://github.com/agshumate/Liftoff

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:52:08 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fliftoff/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/liftoff/blobs/sha256:c3a7ab55b8772ca927e6a1022f62c2e3efa9147a4377f9c85e819ef0bd3033ea
Size	3.0 KB
Checksum	sha256:c3a7ab55b8772ca927e6a1022f62c2e3efa9147a4377f9c85e819ef0bd3033ea
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:52:08 (UTC)		1	3.0 KB	-