modules/kleborate

Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC).

screenassemblyKlebsiellapneumoniae

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

Description

Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC).

Input

name:type

description

pattern

`meta{:bash}`
`:map`

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

`fastas{:bash}`
`:list`

Klebsiella genome assemblies to be screened

*.fasta

Output

name:type

description

pattern

`txt{:bash}`

`meta{:bash}`
`:map`

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

`*.txt{:bash}`
`:file`

Result file generated after screening

*.txt

`versions{:bash}`

`versions.yml{:bash}`
`:file`

File containing software versions

versions.yml

Tools

kleborate
GPL v3 or later (GPL v3+)

Screening Klebsiella genome assemblies for MLST, sub-species, and other Klebsiella related genes of interest

github.com/katholt/Kleborate github.com/katholt/Kleborate/wiki https://github.com/katholt/Kleborate 10.1038/s41467-021-24448-3

modules/kleborate

Description

Input

`meta{:bash}`
`:map`

`fastas{:bash}`
`:list`

Output

`txt{:bash}`

`meta{:bash}`
`:map`

`*.txt{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

kleborate
GPL v3 or later (GPL v3+)

maintainers

get in touch

modules/kleborate

Description

Input

meta{:bash}:map

fastas{:bash}:list

Output

txt{:bash}

meta{:bash}:map

*.txt{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

kleborate GPL v3 or later (GPL v3+)

maintainers

get in touch

`meta{:bash}`
`:map`

`fastas{:bash}`
`:list`

`txt{:bash}`

`meta{:bash}`
`:map`

`*.txt{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

kleborate
GPL v3 or later (GPL v3+)