nf-core_modules/modules/hamronization/summarize/meta.yml

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name: hamronization_summarize
description: Tool to summarize and combine all hAMRonization reports into a single file
keywords:
- amr
- antimicrobial resistance
- reporting
tools:
- hamronization:
description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
tool_dev_url: https://github.com/pha4ge/hAMRonization
doi: ""
licence: ["GNU Lesser General Public v3 (LGPL v3)"]
input:
- reports:
type: file
description: List of multiple hAMRonization reports in either JSON or TSV format
pattern: "*.{json,tsv}"
- format:
type: value
description: Type of final combined report file to be produced
pattern: "tsv|json|interactive"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- json:
type: file
description: hAMRonised summary in JSON format
pattern: "*.json"
- tsv:
type: file
description: hAMRonised summary in TSV format
pattern: "*.json"
- html:
type: file
description: hAMRonised summary in HTML format
pattern: "*.html"
authors:
- "@jfy133"