nf-core_modules/modules/hicap/meta.yml

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name: hicap
description: Identify cap locus serotype and structure in your Haemophilus influenzae assemblies
keywords:
- fasta
- serotype
- Haemophilus influenzae
tools:
- hicap:
description: In silico typing of the H. influenzae capsule locus
homepage: https://github.com/scwatts/hicap
documentation: https://github.com/scwatts/hicap
tool_dev_url: https://github.com/scwatts/hicap
doi: "https://doi.org/10.1128/JCM.00190-19"
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: FASTA formatted assembly file
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
- database_dir:
type: directory
description: Optional - Directory containing locus database
pattern: "*/*"
- model_fp:
type: file
description: Optional - Prodigal model to use for gene prediction
pattern: "*.{bin}"
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"
- gbk:
type: file
description: GenBank file and cap locus annotations
pattern: "*.gbk"
- svg:
type: file
description: Visualization of annotated cap locus
pattern: "*.svg"
- tsv:
type: file
description: Detailed summary of cap locus annotations
pattern: "*.tsv"
authors:
- "@rpetit3"