Description

Tool to convert and summarize ABRicate outputs using the hAMRonization specification

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

report (file)

Output TSV or CSV file from ABRicate

*.{csv,tsv}

format (value)

Type of report file to be produced

tsv|json

software_version (value)

Version of ABRicate used

[0-9].[0-9].[0-9]

reference_db_version (value)

Database version of ABRicate used

[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[0-9][0-9]

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

json (file)

hAMRonised report in JSON format

*.json

tsv (file)

hAMRonised report in TSV format

*.json
included in
funcscan
author
Github user jasmezz
get in touch
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Tools

hamronization
GNU Lesser General Public v3 (LGPL v3)

Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification

github.com/pha4ge/hAMRonization https://github.com/pha4ge/hAMRonization