Description

Tool to convert and summarize AMRfinderPlus 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 file from AMRfinderPlus

*.tsv

format:string

Type of report file to be produced

tsv|json

software_version:string

Version of AMRfinder used

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

reference_db_version:string

Database version of ncbi_AMRfinder used

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

Output

name:type
description
pattern

json

meta:map

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

]

*.json:file

hAMRonised report in JSON format

*.json

tsv

meta:map

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

]

*.tsv:file

hAMRonised report in TSV format

*.tsv

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 louperelo
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