modules/gecco_run

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).

bgcdetectionmetagenomicscontigs

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

Description

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).

Input

name:type

description

pattern

`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

name:type

description

pattern

`genes`

`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

`features`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.features.tsv`
`:file`

TSV file containing identified domains

*.features.tsv

`clusters`

`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

`gbk`

`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

`json`

`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

`versions_gecco`

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

The name of the process

`gecco`
`:string`

The name of the tool

`gecco -V |& sed 's/gecco //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`gecco`
`:string`

The name of the tool

`gecco -V |& sed 's/gecco //'`
`:eval`

The expression to obtain the version of the tool

Tools

gecco
GPL v3

Biosynthetic Gene Cluster prediction with Conditional Random Fields.

gecco.embl.de https://github.com/zellerlab/GECCO 10.1101/2021.05.03.442509

modules/gecco_run

Description

Input

`meta`
`:map`

`input`
`:file`

`hmm`
`:file`

`model_dir`
`:directory`

Output

`genes`

`meta`
`:map`

`*.genes.tsv`
`:file`

`features`

`meta`
`:map`

`*.features.tsv`
`:file`

`clusters`

`meta`
`:map`

`*.clusters.tsv`
`:file`

`gbk`

`meta`
`:map`

`_cluster_.gbk`
`:file`

`json`

`meta`
`:map`

`*.json`
`:file`

`versions_gecco`

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

`gecco`
`:string`

`gecco -V |& sed 's/gecco //'`
`:eval`

Topics

`versions`

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

`gecco`
`:string`

`gecco -V |& sed 's/gecco //'`
`:eval`

Tools

gecco
GPL v3

included in

maintainer

get in touch

modules/gecco_run

Description

Input

meta:map

input:file

hmm:file

model_dir:directory

Output

genes

meta:map

*.genes.tsv:file

features

meta:map

*.features.tsv:file

clusters

meta:map

*.clusters.tsv:file

gbk

meta:map

*_cluster_*.gbk:file

json

meta:map

*.json:file

versions_gecco

${task.process}:string

gecco:string

gecco -V |& sed 's/gecco //':eval

Topics

versions

${task.process}:string

gecco:string

gecco -V |& sed 's/gecco //':eval

Tools

gecco GPL v3

included in

maintainer

get in touch

`meta`
`:map`

`input`
`:file`

`hmm`
`:file`

`model_dir`
`:directory`

`genes`

`meta`
`:map`

`*.genes.tsv`
`:file`

`features`

`meta`
`:map`

`*.features.tsv`
`:file`

`clusters`

`meta`
`:map`

`*.clusters.tsv`
`:file`

`gbk`

`meta`
`:map`

`_cluster_.gbk`
`:file`

`json`

`meta`
`:map`

`*.json`
`:file`

`versions_gecco`

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

`gecco`
`:string`

`gecco -V |& sed 's/gecco //'`
`:eval`

`versions`

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

`gecco`
`:string`

`gecco -V |& sed 's/gecco //'`
`:eval`

gecco
GPL v3