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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
62 lines
2 KiB
YAML
62 lines
2 KiB
YAML
name: gubbins
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description:
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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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licence: ["GPL-2.0-only"]
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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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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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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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