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

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

This command helps transforming the output files created by GECCO into helpful format, should you want to use the results in combination with other tools.

bgc reformatting clusters gbk gff bigslice faa fna

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @vagkaratzas

Maintainers: @vagkaratzas

Summary

This command helps transforming the output files created by GECCO into helpful format, should you want to use the results in combination with other tools.

Get started

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

include { GECCO_CONVERT } from 'nf-core/gecco/convert'

License

MIT License

Process

`Name`	`GECCO_CONVERT`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`clusters` file	TSV file containing coordinates of gecco predicted clusters and BGC types. `*.clusters.tsv`
`gbk` file	Per cluster GenBank file containing sequence with annotations `*.gbk`

`mode` string	Either clusters or gbk folder output, depending on what is reformatted

`format` string	Format for the output file

Output 5 channels

#1 faa tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}/*.faa` file	Amino-acid FASTA converted GenBank files of all the proteins in a cluster `*.faa`

#2 fna tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}/*.fna` file	Nucleotide sequence FASTA converted GenBank files from the cluster `*.fna`

#3 gff tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}/*.gff` file	GFF3 converted cluster tables containing the position and metadata for all the predicted clusters `*.gff`

#4 bigslice tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}/.region.gbk` file	Converted and aliased GenBank files so that they can be loaded by BiG-SLiCE `.region.gbk`

#5 versions

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

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 18:43:35 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgecco%2Fconvert/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gecco/convert/blobs/sha256:5a58834fe6bcdd695839fdabe797323c0634e03725e4c0359f68a8845c5b3f61
Size	3.1 KB
Checksum	sha256:5a58834fe6bcdd695839fdabe797323c0634e03725e4c0359f68a8845c5b3f61
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:43:35 (UTC)		1	3.1 KB	-