Nextflow Registry | nf-core/gecco/run@0.0.0-0c7146d

nf-core/gecco/run @ 0.0.0-0c7146d

GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs).

bgc detection metagenomics contigs

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @jfy133

Maintainers: @jfy133

Summary

GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs).

Get started

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

include { GECCO_RUN } from 'nf-core/gecco/run'

License

MIT License

Process

`Name`	`GECCO_RUN`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	A genomic file containing one or more sequences as input. Input type is any supported by Biopython (fasta, gbk, etc.) `*`
`hmm` file	Alternative HMM file(s) to use in HMMER format `*.hmm`

`model_dir` directory	Path to an alternative CRF (Conditional Random Fields) module to use

Output 6 channels

#1 gbk tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`_cluster_.gbk` file	Per cluster GenBank file (if found) containing sequence with annotations. Will not be generated if no hits are found. `*.gbk`

#2 json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.json` file	AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied. Will not be generated if no hits are found. `*.gbk`

#3 genes tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.genes.tsv` file	TSV file containing detected/predicted genes with BGC probability scores. Will not be generated if no hits are found. `*.genes.tsv`

#4 clusters tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.clusters.tsv` file	TSV file containing coordinates of predicted clusters and BGC types. Will not be generated if no hits are found. `*.clusters.tsv`

#5 features tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.features.tsv` file	TSV file containing identified domains `*.features.tsv`

#6 versions_gecco tuple

`${task.process}` string	The name of the process
`gecco` string	The name of the tool
`gecco -V \| cut -d" " -f2` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
gecco	Biosynthetic Gene Cluster prediction with Conditional Random Fields.	https://gecco.embl.de

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:43:37 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgecco%2Frun/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gecco/run/blobs/sha256:94310a91404d7f52e895f1c05623aaf8e95236a621db6bb462c38a0722c27b8a
Size	3.2 KB
Checksum	sha256:94310a91404d7f52e895f1c05623aaf8e95236a621db6bb462c38a0722c27b8a
Downloads	1

Version	Date	Status	Downloads	Size	Diff