Nextflow Registry | nf-core/plastid/metagene

nf-core/plastid/metagene_generate @ 0.0.0-0c7146d

Compute a metagene profile of read alignments, counts, or quantitative data over one or more regions of interest, optionally applying a mapping rule

genomics riboseq psite

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @suhrig

Maintainers: @suhrig

Compute a metagene profile of read alignments, counts, or quantitative data over one or more regions of interest, optionally applying a mapping rule

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

include { PLASTID_METAGENE_GENERATE } from 'nf-core/plastid/metagene_generate'

MIT License

Process

`Name`	`PLASTID_METAGENE_GENERATE`

Input 1 channel

#1 tuple

`meta` map	Map containing reference information for the reference genome annotation file e.g. `[ id:'Ensembl human v.111' ]`
`annotation` file	annotation file of reference genome (BED, bigBed, GTF, GFF3) `*.{bed,bigbed,gtf,gff3}`

Output 3 channels

#1 rois_bed tuple

`meta` map	Map containing reference information for the reference genome annotation file e.g. `[ id:'Ensembl human v.111' ]`
`*_rois.bed` file	Maximal spanning windows in BED format for visualization in a genome browser. The thickly-rendered portion of a window indicates its landmark. `*_rois.bed`

#2 rois_txt tuple

`meta` map	Map containing reference information for the reference genome annotation file e.g. `[ id:'Ensembl human v.111' ]`
`*_rois.txt` file	Tab-delimited text file describing the maximal spanning window for each gene `*_rois.txt`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
plastid	Nucleotide-resolution analysis of next-generation sequencing and genomics data	https://github.com/joshuagryphon/plastid

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:03:28 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fplastid%2Fmetagene_generate/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/plastid/metagene_generate/blobs/sha256:fe2bcaf05ca9137b4e8d5d676d089b0c6308c3152abf9f01505f900191e2bd72
Size	2.5 KB
Checksum	sha256:fe2bcaf05ca9137b4e8d5d676d089b0c6308c3152abf9f01505f900191e2bd72
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:03:28 (UTC)		1	2.5 KB	-