nf-core/gffread @ 0.0.0-be790aa
Summary
Validate, filter, convert and perform various other operations on GFF files
Get started
Add the following snippet to your workflow script to include this module.
include { GFFREAD } from 'nf-core/gffread'
License
MIT License
Name
|
GFFREAD |
|---|
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}
|
|---|
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
|
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}
|
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
|
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
|
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-be790aa |
|---|---|
| Commit ID | be790aafaa178554b403f862164eb27042f0b35a |
| Release Date | 24 Apr 2026 15:00:49 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgffread/0.0.0-be790aa/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gffread/blobs/sha256:bc19aa45c6d004e837c2c5f98409371457dd11ad13d27f2a78727632ab8b63d5 |
| Size | 3.6 KB |
| Checksum | sha256:bc19aa45c6d004e837c2c5f98409371457dd11ad13d27f2a78727632ab8b63d5 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-be790aa | 24 Apr 2026 15:00:49 (UTC) | 1 | 3.6 KB | |
| 0.0.0-6c4ed3a | 23 Apr 2026 15:21:27 (UTC) | 2 | 3.3 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:13:59 (UTC) | 1 | 3.4 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:06:09 (UTC) | 1 | 3.3 KB |