Nextflow Registry | nf-core/gedi/indexgenome@0.0.0-eac429d

nf-core/gedi/indexgenome @ 0.0.0-eac429d

Build a GEDI genome index from a FASTA and GTF for downstream PRICE ORF prediction

riboseq index genome gedi price orf

Latest version: 0.0.0-eac429d

Total downloads: 0

Source: nf-core/modules

Authors: @pinin4fjords

Maintainers: @pinin4fjords

Build a GEDI genome index from a FASTA and GTF for downstream PRICE ORF prediction

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

include { GEDI_INDEXGENOME } from 'nf-core/gedi/indexgenome'

MIT License

Process

`Name`	`GEDI_INDEXGENOME`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing reference information e.g. `[ id:'homo_sapiens' ]`
`fasta` file	Genome FASTA file `*.{fa,fasta,fna}`
`gtf` file	GTF annotation file `*.{gtf}`

Output 2 channels

#1 index tuple

`meta` map	Groovy Map containing reference information e.g. `[ id:'homo_sapiens' ]`
`${prefix}` directory	GEDI genome index directory containing the `.oml` index file and its sidecar resources. Consumed as `-genomic` by PRICE. Directory name defaults to `meta.id` and can be overridden via `task.ext.prefix`. `*`

#2 versions_gedi tuple

`${task.process}` string	The name of the process
`gedi` string	The name of the tool
`gedi -e Version 2>&1 \| sed -n 's/.Gedi version $[^ ]$.*/\1/p' \| head -n 1` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
gedi	Gedi is a Java software platform for working with genomic data (sequencing reads, sequences, per-base numeric values, annotations). It provides the PRICE algorithm for ribosome profiling ORF discovery.	https://github.com/erhard-lab/gedi

Version	0.0.0-eac429d
Commit ID	eac429d4c67ac5114ce7d4287d460d8f05fd9fab
Release Date	20 May 2026 15:01:17 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgedi%2Findexgenome/0.0.0-eac429d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gedi/indexgenome/blobs/sha256:ea4c38667819bc7024f195c5a82b3c8689efdd605dbb311c0aff144c16054584
Size	2.7 KB
Checksum	sha256:ea4c38667819bc7024f195c5a82b3c8689efdd605dbb311c0aff144c16054584
Downloads	0

Version	Date	Status	Downloads	Size	Diff
0.0.0-eac429d	20 May 2026 15:01:17 (UTC)		0	2.7 KB	-