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 (string)

Type of report file to be produced

tsv|json

software_version (string)

Version of ABRicate used

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

reference_db_version (string)

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
maintainer
Github user jasmezz
get in touch
Ask a question on Slack Open an issue on GitHub

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