Nextflow Registry | nf-core/transdecoder/predict@0.0.0-0c7146d

nf-core/transdecoder/predict @ 0.0.0-0c7146d

TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf

eukaryotes gff cds transcroder

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @Danilo2771

Maintainers: @Danilo2771

Summary

TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf

Get started

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

include { TRANSDECODER_PREDICT } from 'nf-core/transdecoder/predict'

License

MIT License

Process

`Name`	`TRANSDECODER_PREDICT`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	fasta file `*.{fasta}`

`fold` directory	Output from the module transdecoder_longorf `*`

Output 5 channels

#1 bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transdecoder.bed` file	bed file `*{bed}`

#2 cds tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transdecoder.cds` file	the nucleotide coding sequence for all detected ORFs `*{cds}`

#3 pep tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transdecoder.pep` file	All ORFs meeting the minimum length criteria, regardless of coding potential `*.{pep}`

#4 gff3 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transdecoder.gff3` file	Positions of all ORFs as found in the target transcripts `*.{gff3}`

#5 versions

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

Tool	Description	Homepage
transdecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	https://github.com/TransDecoder

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:19:51 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ftransdecoder%2Fpredict/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/transdecoder/predict/blobs/sha256:db0c673cc34ef8376ecf8c1bb40c4bfcd48fa335bbfc4c8470c7776b7009cde4
Size	2.9 KB
Checksum	sha256:db0c673cc34ef8376ecf8c1bb40c4bfcd48fa335bbfc4c8470c7776b7009cde4
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:19:51 (UTC)		1	2.9 KB	-