nf-core_modules/modules/gecco/run/meta.yml
James A. Fellows Yates 9d7208504d
Add gecco/run module (#1790)
* Add gecco/run module

* Fix container URLs

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
2022-06-22 13:43:45 +02:00

67 lines
2.1 KiB
YAML

name: "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).
keywords:
- bgc
- detection
- metagenomics
- contigs
tools:
- "gecco":
description: "Biosynthetic Gene Cluster prediction with Conditional Random Fields."
homepage: "https://gecco.embl.de"
documentation: "https://gecco.embl.de"
tool_dev_url: "https://github.com/zellerlab/GECCO"
doi: "10.1101/2021.05.03.442509"
licence: "['GPL v3']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: A genomic file containing one or more sequences as input. Input type is any supported by Biopython (fasta, gbk, etc.)
pattern: "*"
- hmm:
file: file
description: Alternative HMM file(s) to use in HMMER format
pattern: "*.hmm"
- model_dir:
file: directory
description: Path to an alternative CRF (Conditional Random Fields) module to use
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- genes:
type: file
description: TSV file containing detected/predicted genes with BGC probability scores
pattern: "*.genes.tsv"
- features:
type: file
description: TSV file containing identified domains
pattern: "*.features.tsv"
- clusters:
type: file
description: TSV file containing coordinates of predicted clusters and BGC types
pattern: "*.clusters.tsv"
- gbk:
type: file
description: Per cluster GenBank file (if found) containing sequence with annotations
pattern: "*.gbk"
- json:
type: file
description: AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied
pattern: "*.gbk"
authors:
- "@jfy133"