modules/mmseqs_taxonomy

Computes the lowest common ancestor by identifying the query sequence homologs against the target database.

protein sequencenucleotide sequencedatabasestaxonomyhomologsmmseqs2

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

Description

Computes the lowest common ancestor by identifying the query sequence homologs against the target database.

Input

name:type

description

pattern

`meta`
`:map`

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

`db_query`
`:directory`

An MMseqs2 database with query data

`db_target`
`:directory`

an MMseqs2 database with target data including the taxonomy classification

Output

name:type

description

pattern

`db_taxonomy`

`meta`
`:map`

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

`${prefix}_taxonomy`
`:directory`

An MMseqs2 database with target data including the taxonomy classification

`versions_mmseqs`

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

The name of the process

`mmseqs`
`:string`

The name of the tool

`mmseqs version`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`mmseqs`
`:string`

The name of the tool

`mmseqs version`
`:eval`

The expression to obtain the version of the tool

Tools

mmseqs
GPL v3

MMseqs2: ultra fast and sensitive sequence search and clustering suite

github.com/soedinglab/MMseqs2 mmseqs.com/latest/userguide.pdf https://github.com/soedinglab/MMseqs2 10.1093/bioinformatics/btw006

modules/mmseqs_taxonomy

Description

Input

`meta`
`:map`

`db_query`
`:directory`

`db_target`
`:directory`

Output

`db_taxonomy`

`meta`
`:map`

`${prefix}_taxonomy`
`:directory`

`versions_mmseqs`

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

`mmseqs`
`:string`

`mmseqs version`
`:eval`

Topics

`versions`

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

`mmseqs`
`:string`

`mmseqs version`
`:eval`

Tools

mmseqs
GPL v3

included in

maintainer

get in touch

modules/mmseqs_taxonomy

Description

Input

meta:map

db_query:directory

db_target:directory

Output

db_taxonomy

meta:map

${prefix}_taxonomy:directory

versions_mmseqs

${task.process}:string

mmseqs:string

mmseqs version:eval

Topics

versions

${task.process}:string

mmseqs:string

mmseqs version:eval

Tools

mmseqs GPL v3

included in

maintainer

get in touch

`meta`
`:map`

`db_query`
`:directory`

`db_target`
`:directory`

`db_taxonomy`

`meta`
`:map`

`${prefix}_taxonomy`
`:directory`

`versions_mmseqs`

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

`mmseqs`
`:string`

`mmseqs version`
`:eval`

`versions`

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

`mmseqs`
`:string`

`mmseqs version`
`:eval`

mmseqs
GPL v3