Description

Tool to convert and summarize DeepARG 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 .mapping.ARG file from DeepARG

*.mapping.ARG

format:string

Type of report file to be produced

tsv|json

software_version:string

Version of DeepARG used

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

reference_db_version:integer

Database version of DeepARG used

[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 jfy133
Ask a question on Slack Open an issue on GitHub