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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
61 lines
2 KiB
YAML
61 lines
2 KiB
YAML
name: gubbins
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description: Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies
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loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the
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putative point mutations outside of these regions.
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keywords:
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- recombination
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- alignment
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tools:
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- gubbins:
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description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
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homepage: https://sanger-pathogens.github.io/gubbins/
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documentation: https://sanger-pathogens.github.io/gubbins/
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input:
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- alignment:
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type: file
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description: fasta alignment file
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pattern: "*.{fasta,fas,fa,aln}"
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output:
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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- fasta:
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type: file
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description: Filtered variant alignment in fasta format
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pattern: "*.{fasta}"
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- embl_predicted:
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type: file
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description: Recombination predictions in embl format
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pattern: "*.{recombination_predictions.embl}"
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- gff:
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type: file
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description: Recombination predictions in gff format
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pattern: "*.{gff}"
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- embl_branch:
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type: file
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description: Branch base reconstruction
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pattern: "*.{branch_base_reconstruction.embl}"
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- vcf:
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type: file
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description: SNP distribution
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pattern: "*.{vcf}"
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- stats:
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type: file
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description: Per branch statistics
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pattern: "*.{csv}"
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- phylip:
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type: file
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description: Filtered variant alignment in phylip format
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pattern: "*.{phylip}"
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- tree:
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type: file
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description: Recombination removed RAxML phylogenetic tree
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pattern: "*.{final_tree.tre}"
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- tree_labelled:
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type: file
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description: Recombination removed RAxML phylogenetic tree (nodes labelled)
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pattern: "*.{node_labelled.final_tree.tre}"
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authors:
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- "@avantonder"
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