modules/abritamr_run

A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes

bacteriafastaantibiotic resistance

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

Description

A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes

Input

name:type

description

pattern

`meta:map`

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

`fasta:file`

Assembled contigs in FASTA format

*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}

Output

name:type

description

pattern

`matches`

`meta:file`

Tab-delimited file, with a row per sequence, and columns representing functional drug classes

*.summary_matches.txt

`${prefix}.summary_matches.txt:file`

Tab-delimited file, with a row per sequence, and columns representing functional drug classes

*.summary_matches.txt

`partials`

`meta:file`

Tab-delimited file, with a row per sequence, and columns representing partial hits to functional drug classes

*.summary_partials.txt

`${prefix}.summary_partials.txt:file`

Tab-delimited file, with a row per sequence, and columns representing partial hits to functional drug classes

*.summary_partials.txt

`virulence`

`meta:string`

Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification

*.summary_virulence.txt

`${prefix}.summary_virulence.txt:string`

Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification

*.summary_virulence.txt

`out`

`meta:string`

raw output from AMRFinder plus (per sequence)

*.amrfinder.txt

`${prefix}.amrfinder.out:string`

raw output from AMRFinder plus (per sequence)

*.amrfinder.txt

`txt`

`meta:string`

Tab-delimited file, combining non-empty summary files

*.abritamr.txt

`${prefix}.abritamr.txt:string`

Tab-delimited file, combining non-empty summary files

*.abritamr.txt

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

abritamr
GPL v3

A pipeline for running AMRfinderPlus and collating results into functional classes

github.com/MDU-PHL/abritamr 10.1038/s41467-022-35713-4

modules/abritamr_run

Description

Input

`meta:map`

`fasta:file`

Output

`matches`

`meta:file`

`${prefix}.summary_matches.txt:file`

`partials`

`meta:file`

`${prefix}.summary_partials.txt:file`

`virulence`

`meta:string`

`${prefix}.summary_virulence.txt:string`

`out`

`meta:string`

`${prefix}.amrfinder.out:string`

`txt`

`meta:string`

`${prefix}.abritamr.txt:string`

`versions`

`versions.yml:file`

Tools

abritamr
GPL v3

maintainer

get in touch

modules/abritamr_run

Description

Input

meta:map

fasta:file

Output

matches

meta:file

${prefix}.summary_matches.txt:file

partials

meta:file

${prefix}.summary_partials.txt:file

virulence

meta:string

${prefix}.summary_virulence.txt:string

out

meta:string

${prefix}.amrfinder.out:string

txt

meta:string

${prefix}.abritamr.txt:string

versions

versions.yml:file

Tools

abritamr GPL v3

maintainer

get in touch

`meta:map`

`fasta:file`

`matches`

`meta:file`

`${prefix}.summary_matches.txt:file`

`partials`

`meta:file`

`${prefix}.summary_partials.txt:file`

`virulence`

`meta:string`

`${prefix}.summary_virulence.txt:string`

`out`

`meta:string`

`${prefix}.amrfinder.out:string`

`txt`

`meta:string`

`${prefix}.abritamr.txt:string`

`versions`

`versions.yml:file`

abritamr
GPL v3