modules/repeatmodeler_repeatmodeler

Performs de novo transposable element (TE) family identification with RepeatModeler

genomicsfastarepeattransposable element

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

Description

Performs de novo transposable element (TE) family identification with RepeatModeler

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`db`
`:file`

RepeatModeler database files generated with REPEATMODELER_BUILDDATABASE

*

Output

name:type

description

pattern

`fasta`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.fa`
`:file`

Consensus repeat sequences

*.fa

`stk`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.stk`
`:file`

Seed alignments

*.stk

`log`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.log`
`:file`

A summarized log of the run

*.log

`versions_repeatmodeler`

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

The name of the process

`repeatmodeler`
`:string`

The name of the tool

`RepeatModeler --version 2>&1 | sed 's/RepeatModeler 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

`repeatmodeler`
`:string`

The name of the tool

`RepeatModeler --version 2>&1 | sed 's/RepeatModeler version //'`
`:eval`

The expression to obtain the version of the tool

Tools

repeatmodeler
Open Software License v2.1

RepeatModeler is a de-novo repeat family identification and modeling package.

github.com/Dfam-consortium/RepeatModeler

modules/repeatmodeler_repeatmodeler

Description

Input

`meta`
`:map`

`db`
`:file`

Output

`fasta`

`meta`
`:map`

`*.fa`
`:file`

`stk`

`meta`
`:map`

`*.stk`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_repeatmodeler`

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

`repeatmodeler`
`:string`

`RepeatModeler --version 2>&1 | sed 's/RepeatModeler version //'`
`:eval`

Topics

`versions`

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

`repeatmodeler`
`:string`

`RepeatModeler --version 2>&1 | sed 's/RepeatModeler version //'`
`:eval`

Tools

repeatmodeler
Open Software License v2.1

included in

maintainer

get in touch

modules/repeatmodeler_repeatmodeler

Description

Input

meta :map

db :file

Output

fasta

meta :map

*.fa :file

stk

meta :map

*.stk :file

log

meta :map

*.log :file

versions_repeatmodeler

${task.process} :string

repeatmodeler :string

RepeatModeler --version 2>&1 | sed 's/RepeatModeler version //' :eval

Topics

versions

${task.process} :string

repeatmodeler :string

RepeatModeler --version 2>&1 | sed 's/RepeatModeler version //' :eval

Tools

repeatmodelerOpen Software License v2.1

included in

maintainer

get in touch

`meta`
`:map`

`db`
`:file`

`fasta`

`meta`
`:map`

`*.fa`
`:file`

`stk`

`meta`
`:map`

`*.stk`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_repeatmodeler`

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

`repeatmodeler`
`:string`

`RepeatModeler --version 2>&1 | sed 's/RepeatModeler version //'`
`:eval`

`versions`

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

`repeatmodeler`
`:string`

`RepeatModeler --version 2>&1 | sed 's/RepeatModeler version //'`
`:eval`

repeatmodeler
Open Software License v2.1