modules/argnorm

Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).

amrantimicrobial resistanceargantimicrobial resistance genesgenomicsmetagenomicsnormalizationdrug categorization

https://github.com/nf-core/modules/[...]/modules/nf-core/argnorm

Description

Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`input_tsv:file`

ARG annotation output

*.tsv

`tool:string`

ARG annotation tool used

argsoap|abricate|deeparg|resfinder|amrfinderplus

`db:string`

Database used for ARG annotation

Output

name:type

description

pattern

`tsv`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`*.tsv:file`

Normalized argNorm output

*.tsv

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

argnorm
MIT

Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).

argnorm.readthedocs.io/en/latest https://github.com/BigDataBiology/argNorm

modules/argnorm

Description

Input

meta:map

input_tsv:file

tool:string

db:string

Output

tsv

meta:map

*.tsv:file

versions

versions.yml:file

Tools

argnorm MIT

`meta:map`

`input_tsv:file`

`tool:string`

`db:string`

`tsv`

`meta:map`

`*.tsv:file`

`versions`

`versions.yml:file`

argnorm
MIT