nf-core/ea-utils/gtf2bed @ 0.0.0-56a9b6d
Summary
Convert a GTF/GFF annotation file to BED12 format
Get started
Add the following snippet to your workflow script to include this module.
include { EAUTILS_GTF2BED } from 'nf-core/ea-utils/gtf2bed'
License
MIT License
Process
Name
|
EAUTILS_GTF2BED |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
gtf
file
|
GTF or GFF annotation file *.{gtf,gff,gtf.gz,gff.gz}
|
Output
2 channels
#1
bed
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${prefix}.bed
file
|
BED12 format annotation file with one entry per transcript *.bed
|
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| gtf2bed | Perl script from the ea-utils package that converts GTF/GFF annotation files to BED12 format, handling exons, start/stop codons, and miRNAs. Produces UCSC-compatible BED with proper thin/thick regions. | https://expressionanalysis.github.io/ea-utils/ |
| Version | 0.0.0-56a9b6d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 10 Apr 2026 15:00:29 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fea-utils%2Fgtf2bed/0.0.0-56a9b6d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/ea-utils/gtf2bed/blobs/sha256:e5157474df6bba91b7ed4d65eaf244e158ebc4a9717a550bbf1cd3a4500d0ef8 |
| Size | 4.5 KB |
| Checksum | sha256:e5157474df6bba91b7ed4d65eaf244e158ebc4a9717a550bbf1cd3a4500d0ef8 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:14:34 (UTC) | 4 | 4.5 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:10:35 (UTC) | 3 | 4.5 KB | |
| 0.0.0-c24122a | 11 Apr 2026 15:00:30 (UTC) | 4 | 4.5 KB | |
| 0.0.0-56a9b6d | 10 Apr 2026 15:00:29 (UTC) | 4 | 4.5 KB |