Nextflow Registry | nf-core/custom/tx2gene@0.0.0-0c7146d

nf-core/custom/tx2gene @ 0.0.0-0c7146d

Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications.

gene gtf pseudoalignment rsem transcript

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @pinin4fjords

Maintainers: @pinin4fjords

Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications.

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

include { CUSTOM_TX2GENE } from 'nf-core/custom/tx2gene'

MIT License

Process

`Name`	`CUSTOM_TX2GENE`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing reference information related to the GTF file e.g. `[ id:'yeast' ]`
`gtf` file	An annotation file of the reference genome in GTF format `*.gtf`

#2 tuple

`meta2` map	Groovy Map containing information related to the experiment as a whole e.g. `[ id:'SRP123456' ]`
`quants/*` file	quants file

`quant_type` string	Quantification type, 'kallisto', 'salmon', or 'rsem'

`id` string	Gene ID attribute in the GTF file (default= gene_id)

`extra` string	Extra gene attribute(s) in the GTF file, comma-separated for multiple (default= gene_name)

Output 2 channels

#1 tx2gene tuple

`meta` map	Groovy Map containing reference information related to the GTF file e.g. `[ id:'yeast' ]`
`*tx2gene.tsv` file	A transcript/ gene mapping table in TSV format `*.tx2gene.tsv`

#2 versions

`versions.yml` file	YAML file containing versions of tools used in the module

Tool	Description	Homepage
custom	"Custom module to create a transcript to gene mapping from a GTF and check it against transcript quantifications"	n/a

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:34:12 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcustom%2Ftx2gene/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/custom/tx2gene/blobs/sha256:03eaf4b9f38c9d48cb70a439a62514c3bba2934ec6283c0aaec4835209800222
Size	5.5 KB
Checksum	sha256:03eaf4b9f38c9d48cb70a439a62514c3bba2934ec6283c0aaec4835209800222
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:34:12 (UTC)		1	5.5 KB	-