Nextflow Registry | nf-core/gstama/merge@0.0.0-0c7146d

nf-core/gstama/merge @ 0.0.0-0c7146d

Merge multiple transcriptomes while maintaining source information.

gstama gstama/merge long-read isoseq nanopore tama trancriptome annotation

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @sguizard

Maintainers: @sguizard

Summary

Merge multiple transcriptomes while maintaining source information.

Get started

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

include { GSTAMA_MERGE } from 'nf-core/gstama/merge'

License

MIT License

Process

`Name`	`GSTAMA_MERGE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bed` file	bed12 file generated by TAMA collapse `*.bed`

`filelist` file	list of files

Output 5 channels

#1 bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.bed` file	This is the main merged annotation file. Transcripts are coloured according to the source support for each model. Sources are numbered based on the order supplied in the input filelist file. For example the first file named in the filelist file would have its transcripts coloured in red. If a transcript has multiple sources the colour is shown as magenta. `*.bed`

#2 merge tuple

meta map

Groovy Map containing sample information e.g. [ id:'test' ]

*_merge.txt file

This contains a bed12 format file which shows the coordinates of each input transcript matched to the merged transcript ID. I used the "txt" extension even though it is a bed file just to avoid confusion with the main bed file. You can use this file to map the final merged transcript models to their pre-merged supporting transcripts. The 1st subfield in the 4th column shows the final merged transcript ID while the 2nd subfield shows the pre-merged transcript ID with source prefix.

*_merge.txt

#3 versions

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

#4 gene_report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*_gene_report.txt` file	This contains a report of the genes from the merged file. "num_clusters" refers to the number of source transcripts that were used to make this gene model. "num_final_trans" refers to the number of transcripts in the final gene model. `*_gene_report.txt`

#5 trans_report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*_trans_report.txt` file	This contains the source information for each merged transcript. `*_trans_report.txt`

Tool	Description	Homepage
gstama	Gene-Switch Transcriptome Annotation by Modular Algorithms	https://github.com/sguizard/gs-tama

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:45:32 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgstama%2Fmerge/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gstama/merge/blobs/sha256:2318bbf748119c048e0b8a347bd9f6627f69eedeca6669d59a6b13533e3f5f81
Size	3.6 KB
Checksum	sha256:2318bbf748119c048e0b8a347bd9f6627f69eedeca6669d59a6b13533e3f5f81
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:45:32 (UTC)		1	3.6 KB	-