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

nf-core/gffread @ 0.0.0-0c7146d

Validate, filter, convert and perform various other operations on GFF files

gff conversion validation

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @edmundmiller

Maintainers: @edmundmiller @gallvp

Validate, filter, convert and perform various other operations on GFF files

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

include { GFFREAD } from 'nf-core/gffread'

MIT License

Process

`Name`	`GFFREAD`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test' ]
`gff` file	A reference file in either the GFF3, GFF2 or GTF format. `*.{gff, gtf}`

`fasta` file	A multi-fasta file with the genomic sequences `*.{fasta,fa,faa,fas,fsa}`

Output 5 channels

#1 bed tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test' ]
`*.bed` file	BED file resulting from the conversion of the GFF input file when the '--bed' argument is present `*.bed`

#2 gtf tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test' ]
`*.gtf` file	GTF file resulting from the conversion of the GFF input file if '-T' argument is present `*.{gtf}`

#3 gffread_gff tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test' ]
`*.gff3` file	GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent `*.gff3`

#4 gffread_fasta tuple

`meta` map	Groovy Map containing meta data e.g. [ id:'test' ]
`*.fasta` file	Fasta file produced when either of '-w', '-x', '-y' parameters is present `*.fasta`

#5 versions_gffread tuple

`${task.process}` string	The process the versions were collected from
`gffread` string	The tool name
`gffread --version 2>&1` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
gffread	GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread

Version	0.0.0-0c7146d
Commit ID	8098ab9d800821e8b18e17fd515ed1e4ebc523f4
Release Date	08 Apr 2026 18:44:35 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgffread/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gffread/blobs/sha256:2b6502ff6ccbec41942fb02c9b788e2773befe90ad56b572c8e6615b86450466
Size	3.3 KB
Checksum	sha256:2b6502ff6ccbec41942fb02c9b788e2773befe90ad56b572c8e6615b86450466
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:44:35 (UTC)		1	3.3 KB	-