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`
`:map`

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

`fastas`
`:list`

Klebsiella genome assemblies to be screened

*.fasta

Output

name:type

description

pattern

`txt`

`meta`
`:map`

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

`*.txt`
`:file`

Result file generated after screening

*.txt

`versions_kleborate`

`${task.process}`
`:string`

The name of the process

`kleborate`
`:string`

The name of the tool

`kleborate --version | sed 's/Kleborate v//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`kleborate`
`:string`

The name of the tool

`kleborate --version | sed 's/Kleborate v//'`
`:eval`

The expression to obtain the version of the tool

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`
`:map`

`fastas`
`:list`

Output

`txt`

`meta`
`:map`

`*.txt`
`:file`

`versions_kleborate`

`${task.process}`
`:string`

`kleborate`
`:string`

`kleborate --version | sed 's/Kleborate v//'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`kleborate`
`:string`

`kleborate --version | sed 's/Kleborate v//'`
`:eval`

Tools

kleborate
GPL v3 or later (GPL v3+)

maintainers

get in touch

modules/kleborate

Description

Input

meta :map

fastas :list

Output

txt

meta :map

*.txt :file

versions_kleborate

${task.process} :string

kleborate :string

kleborate --version | sed 's/Kleborate v//' :eval

Topics

versions

${task.process} :string

kleborate :string

kleborate --version | sed 's/Kleborate v//' :eval

Tools

kleborateGPL v3 or later (GPL v3+)

maintainers

get in touch

`meta`
`:map`

`fastas`
`:list`

`txt`

`meta`
`:map`

`*.txt`
`:file`

`versions_kleborate`

`${task.process}`
`:string`

`kleborate`
`:string`

`kleborate --version | sed 's/Kleborate v//'`
`:eval`

`versions`

`${task.process}`
`:string`

`kleborate`
`:string`

`kleborate --version | sed 's/Kleborate v//'`
`:eval`

kleborate
GPL v3 or later (GPL v3+)