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

]

`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

]

`*.txt:file`

Result file generated after screening

*.txt

`versions`

`versions.yml: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:map

fastas:list

Output

txt

meta:map

*.txt:file

versions

versions.yml:file

Tools

kleborate GPL v3 or later (GPL v3+)

`meta:map`

`fastas:list`

`txt`

`meta:map`

`*.txt:file`

`versions`

`versions.yml:file`

kleborate
GPL v3 or later (GPL v3+)