modules/bigslice

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 clustersgenomicsanalysis

https://github.com/nf-core/modules/[...]/modules/nf-core/bigslice

Description

Input

name:type

description

pattern

`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

name:type

description

pattern

`output`

`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

`tsv`

`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

`versions_bigslice`

`${task.process}`
`:string`

The name of the process

`bigslice`
`:string`

The name of the tool

`2.0.2`
`:string`

The version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`bigslice`
`:string`

The name of the tool

`2.0.2`
`:string`

The version of the tool

Tools

bigslice
AGPL v3-or-later

A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data

github.com/medema-group/bigslice 10.1093/gigascience/giaa154

modules/bigslice

Description

Input

`meta`
`:map`

`bgc`
`:file`

`hmmdb`
`:directory`

`export_tsv`
`:boolean`

Output

`output`

`meta`
`:map`

`${prefix}/result`
`:directory`

`tsv`

`meta`
`:map`

`${prefix}/result/tsv_export`
`:directory`

`versions_bigslice`

`${task.process}`
`:string`

`bigslice`
`:string`

`2.0.2`
`:string`

Topics

`versions`

`${task.process}`
`:string`

`bigslice`
`:string`

`2.0.2`
`:string`

Tools

bigslice
AGPL v3-or-later

maintainers

get in touch

modules/bigslice

Description

Input

meta :map

bgc :file

hmmdb :directory

export_tsv :boolean

Output

output

meta :map

${prefix}/result :directory

tsv

meta :map

${prefix}/result/tsv_export :directory

versions_bigslice

${task.process} :string

bigslice :string

2.0.2 :string

Topics

versions

${task.process} :string

bigslice :string

2.0.2 :string

Tools

bigsliceAGPL v3-or-later

maintainers

get in touch

`meta`
`:map`

`bgc`
`:file`

`hmmdb`
`:directory`

`export_tsv`
`:boolean`

`output`

`meta`
`:map`

`${prefix}/result`
`:directory`

`tsv`

`meta`
`:map`

`${prefix}/result/tsv_export`
`:directory`

`versions_bigslice`

`${task.process}`
`:string`

`bigslice`
`:string`

`2.0.2`
`:string`

`versions`

`${task.process}`
`:string`

`bigslice`
`:string`

`2.0.2`
`:string`

bigslice
AGPL v3-or-later