Description

Screen assemblies for antimicrobial resistance against multiple databases

Input

name:type
description
pattern

meta:map

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

]

reports:file

FASTA, GenBank or EMBL formatted file

*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}

Output

name:type
description
pattern

report

meta:map

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

]

*.txt:file

Tab-delimited report of aggregated results

*.{txt}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

abricate
GPL v2

Mass screening of contigs for antibiotic resistance genes