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nf-core/gstama/merge @ 0.0.0-6c4ed3a

Merge multiple transcriptomes while maintaining source information.

gstama gstama/merge long-read isoseq nanopore tama trancriptome annotation
Latest version: 0.0.0-6c4ed3a
Total downloads: 9
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 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:22:58 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fgstama%2Fmerge/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gstama/merge/blobs/sha256:a88c5f7977b07c07eb032628913820f1b75a58f39e53d630ea323e0cbd6e61a6
Size 3.6 KB
Checksum sha256:a88c5f7977b07c07eb032628913820f1b75a58f39e53d630ea323e0cbd6e61a6
Downloads 3
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:22:58 (UTC) 3 3.6 KB
0.0.0-3fc6d40 22 Apr 2026 15:14:34 (UTC) 3 3.6 KB
0.0.0-0c7146d 08 Apr 2026 19:07:06 (UTC) 3 3.6 KB