mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
5644df8d43
* Make gene and cluster TSVs optional output in case no hits found * update indicating optional output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
67 lines
2.3 KiB
YAML
67 lines
2.3 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. Will not be generated if no hits are found.
|
|
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. Will not be generated if no hits are found.
|
|
pattern: "*.clusters.tsv"
|
|
- gbk:
|
|
type: file
|
|
Description: Per cluster GenBank file (if found) containing sequence with annotations. Will not be generated if no hits are found.
|
|
pattern: "*.gbk"
|
|
- json:
|
|
type: file
|
|
description: AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied. Will not be generated if no hits are found.
|
|
pattern: "*.gbk"
|
|
|
|
authors:
|
|
- "@jfy133"
|