Nextflow Registry | nf-core/bigslice@0.0.0-3fc6d40

nf-core/bigslice @ 0.0.0-3fc6d40

A scalable tool for large-scale analysis of Biosynthetic Gene Clusters (BGCs). It takes genome regions in GenBank format along with an HMM database and produces a SQLite database and FASTA outputs of predicted features.

biosynthetic gene clusters genomics analysis

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @vagkaratzas @SkyLex

Maintainers: @vagkaratzas @SkyLex

Summary

Get started

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

include { BIGSLICE } from 'nf-core/bigslice'

License

MIT License

Process

`Name`	`BIGSLICE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`bgc` file	List of GenBank (.gbk) files containing genomic region annotations for BiG-SLiCE input. Each file represents a BGC region. The module internally organises them into the required BiG-SLiCE input folder structure (datasets.tsv and taxonomy TSV). `*.gbk`

`hmmdb` directory	Path to the BiG-SLiCE HMM database folder containing biosynthetic and sub Pfams for annotation, in the required BiG-SLiCE format. An example directory in compressed archive format can be found here: https://github.com/medema-group/bigslice/releases/download/v2.0.0rc/bigslice-models.2022-11-30.tar.gz

`export_tsv` boolean	If true, runs a second BiG-SLiCE invocation to export all results from the SQLite database to TSV files under `tsv_export/`. Additional arguments for this step can be passed via `task.ext.args2`.

Output 3 channels

#1 tsv tuple

`meta` map	Groovy Map containing sample/dataset information
`${prefix}/result/tsv_export` directory	Directory containing TSV exports of all parsed BGC metadata, vectorized features and clustering results. Only present when `export_tsv` input is set to `true`. `tsv_export`

#2 output tuple

`meta` map	Groovy Map containing sample/dataset information
`${prefix}/result` directory	BiG-SLiCE result directory containing the SQLite database (`data.db`), predicted feature FASTA files (`tmp/*/.fa`), and optionally TSV exports (`tsv_export/`) when `export_tsv` is `true`. `result`

#3 versions_bigslice tuple

`${task.process}` string	The name of the process
`bigslice` string	The name of the tool
`2.0.2` string	The version of the tool

Tool	Description	Homepage
bigslice	A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data	https://github.com/medema-group/bigslice

Version	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:04:05 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbigslice/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bigslice/blobs/sha256:37d62f1516b2ee97e489e459a4ee9c7768f865056c747661e1a0dd393dc7fa88
Size	3.9 KB
Checksum	sha256:37d62f1516b2ee97e489e459a4ee9c7768f865056c747661e1a0dd393dc7fa88
Downloads	2

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:06:01 (UTC)	4	3.9 KB
0.0.0-3fc6d40	22 Apr 2026 15:04:05 (UTC)	2	3.9 KB
0.0.0-0c7146d	08 Apr 2026 18:47:31 (UTC)	3	3.9 KB