nf-core_modules/modules/scoary/meta.yml

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name: scoary
description: Use pangenome outputs for GWAS
keywords:
- gwas
- pangenome
- prokaryote
tools:
- scoary:
description: Microbial pan-GWAS using the output from Roary
homepage: https://github.com/AdmiralenOla/Scoary
documentation: https://github.com/AdmiralenOla/Scoary
tool_dev_url: https://github.com/AdmiralenOla/Scoary
doi: "10.1186/s13059-016-1108-8"
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- genes:
type: file
description: A presence/absence matrix of genes in the pan-genome
pattern: "*.csv"
- traits:
type: file
description: A CSV file containing trait information per-sample
pattern: "*.csv"
- tree:
type: file
description: A Newick formtted tree for phylogenetic analyses
pattern: "*.{dnd,nwk,treefile}"
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"
- csv:
type: file
description: Gene associations in a CSV file per trait
pattern: "*.csv"
authors:
- "@rpetit3"