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:false ]

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

json

meta:map

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

*.json:file

hAMRonised report in JSON format

*.json

tsv

meta:map

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

*.tsv:file

hAMRonised report in TSV format

*.json

versions

versions.yml:file

File containing software versions

versions.yml

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
funcscan
Github user jasmezz
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