Nextflow Registry | nf-core/gecco/convert@0.0.0-3fc6d40

nf-core/gecco/convert @ 0.0.0-3fc6d40

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: 0.0.0-6c4ed3a

Total downloads: 10

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	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:13:35 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fgecco%2Fconvert/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gecco/convert/blobs/sha256:b6c359d464a69ca5776c6ba494afec386110631c8befc418220ea230634d1da9
Size	3.1 KB
Checksum	sha256:b6c359d464a69ca5776c6ba494afec386110631c8befc418220ea230634d1da9
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:20:50 (UTC)	3	3.1 KB
0.0.0-3fc6d40	22 Apr 2026 15:13:35 (UTC)	3	3.1 KB
0.0.0-0c7146d	08 Apr 2026 19:05:15 (UTC)