nf-core_modules/modules/gubbins/meta.yml

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name: gubbins
description:
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies
loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the
putative point mutations outside of these regions.
licence: ["GPL-2.0-only"]
keywords:
- recombination
- alignment
tools:
- gubbins:
description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
homepage: https://sanger-pathogens.github.io/gubbins/
documentation: https://sanger-pathogens.github.io/gubbins/
input:
- alignment:
type: file
description: fasta alignment file
pattern: "*.{fasta,fas,fa,aln}"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- fasta:
type: file
description: Filtered variant alignment in fasta format
pattern: "*.{fasta}"
- embl_predicted:
type: file
description: Recombination predictions in embl format
pattern: "*.{recombination_predictions.embl}"
- gff:
type: file
description: Recombination predictions in gff format
pattern: "*.{gff}"
- embl_branch:
type: file
description: Branch base reconstruction
pattern: "*.{branch_base_reconstruction.embl}"
- vcf:
type: file
description: SNP distribution
pattern: "*.{vcf}"
- stats:
type: file
description: Per branch statistics
pattern: "*.{csv}"
- phylip:
type: file
description: Filtered variant alignment in phylip format
pattern: "*.{phylip}"
- tree:
type: file
description: Recombination removed RAxML phylogenetic tree
pattern: "*.{final_tree.tre}"
- tree_labelled:
type: file
description: Recombination removed RAxML phylogenetic tree (nodes labelled)
pattern: "*.{node_labelled.final_tree.tre}"
authors:
- "@avantonder"